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Opened 2 days ago
Last modified 43 hours ago
#20538 accepted defect
Problem restoring pseudo bonds in scenes
| Reported by: | Owned by: | Eric Pettersen | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Scenes/Animation | Version: | |
| Keywords: | Cc: | Zach Pearson | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description (last modified by )
The following bug report has been submitted:
Platform: Linux-6.8.0-124-generic-x86_64-with-glibc2.35
ChimeraX Version: 1.12 (2026-06-12 03:42:34 UTC)
Description
Replace this text with list of actions that caused this problem to occur
Log:
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
> open /home/rquiroga/colaboraciones/Eva/paper2.cxs
Log from Thu Jun 25 10:29:56 2026 Startup Messages
---
warning | GBM is not supported with the current configuration. Fallback to Vulkan rendering in Chromium.
UCSF ChimeraX version: 1.12 (2026-06-12)
© 2016-2026 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open 1m27
1m27 title:
Crystal structure of SAP/FynSH3/SLAM ternary complex [more info...]
Chain information for 1m27 #1
---
Chain | Description | UniProt
A | SH2 domain protein 1A | SH21A_HUMAN 1-104
B | Signaling lymphocytic activation molecule | SLAF1_HUMAN 276-286
C | Proto-oncogene tyrosine-protein kinase FYN | FYN_HUMAN 84-144
Non-standard residues in 1m27 #1
---
FLC — citrate anion
> ui tool show OpenFold
> select /A:81
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
72 atoms, 72 bonds, 9 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> open 1m27
1m27 title:
Crystal structure of SAP/FynSH3/SLAM ternary complex [more info...]
Chain information for 1m27 #2
---
Chain | Description | UniProt
A | SH2 domain protein 1A | SH21A_HUMAN 1-104
B | Signaling lymphocytic activation molecule | SLAF1_HUMAN 276-286
C | Proto-oncogene tyrosine-protein kinase FYN | FYN_HUMAN 84-144
Non-standard residues in 1m27 #2
---
FLC — citrate anion
> hide #1 models
> select #2/B:276
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
23 atoms, 22 bonds, 3 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
> select #2/C:111
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
53 atoms, 53 bonds, 6 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> delete atoms sel
> delete bonds sel
Drag select of 1 residues
> select #2/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ILE rotLib Dynameomics
1m27 #2/A PHE 77: phi -144.4, psi 135.0 trans
Changed 45 bond radii
> show sel atoms
> clashes #!2 & ~#!2/A:77 & ~solvent overlapCutoff 0.4 radius 0.075 reveal
> true restrict #2.1 & ~@c,ca,n
39 clashes
> select down
11 atoms, 11 bonds, 1 residue, 1 model selected
Must open a volume/map file first!
> hbonds #!2 & ~#!2/A:77 & ~solvent reveal true restrict #2.1 & ~@c,ca,n
0 hydrogen bonds found
> swapaa #!2/A:77 ILE criteria 7 rotLib Dynameomics
Using Dynameomics library
1m27 #!2/A PHE 77: phi -144.4, psi 135.0 trans
Applying ILE rotamer (chi angles: -61.2 101.7) to 1m27 #!2/A ILE 77
> openfold predict protein #1/A protein #2/A name 1m27_A_F77I
Running OpenFold prediction of 2 proteins with 208 residues on gpu
Using multiple sequence alignment server https://api.colabfold.com
Running openfold prediction failed with exit code 1:
command:
/home/rquiroga/openfold3/bin/run_openfold predict
--query_json=1m27_A_F77I.json --runner_yaml=msa_path.yaml
--num_diffusion_samples=1 --device=gpu
stdout:
stderr:
/home/rquiroga/openfold3/lib/python3.11/site-
packages/torch/cuda/__init__.py:262: UserWarning:
Found GPU0 NVIDIA GeForce GTX 1080 which is of cuda capability 6.1.
PyTorch no longer supports this GPU because it is too old.
The minimum cuda capability supported by this library is 7.5.
warnings.warn(
/home/rquiroga/openfold3/lib/python3.11/site-
packages/torch/cuda/__init__.py:287: UserWarning:
NVIDIA GeForce GTX 1080 with CUDA capability sm_61 is not compatible with the
current PyTorch installation.
The current PyTorch install supports CUDA capabilities sm_75 sm_80 sm_86 sm_90
sm_100 sm_120 compute_120.
If you want to use the NVIDIA GeForce GTX 1080 GPU with PyTorch, please check
the instructions at https://pytorch.org/get-started/locally/
warnings.warn(
/home/rquiroga/openfold3/lib/python3.11/site-
packages/torch/cuda/__init__.py:262: UserWarning:
Found GPU0 NVIDIA GeForce GTX 1080 which is of cuda capability 6.1.
PyTorch no longer supports this GPU because it is too old.
The minimum cuda capability supported by this library is 7.5.
warnings.warn(
/home/rquiroga/openfold3/lib/python3.11/site-
packages/torch/cuda/__init__.py:287: UserWarning:
NVIDIA GeForce GTX 1080 with CUDA capability sm_61 is not compatible with the
current PyTorch installation.
The current PyTorch install supports CUDA capabilities sm_75 sm_80 sm_86 sm_90
sm_100 sm_120 compute_120.
If you want to use the NVIDIA GeForce GTX 1080 GPU with PyTorch, please check
the instructions at https://pytorch.org/get-started/locally/
warnings.warn(
2026-06-24 09:30:27,692 - INFO - Note: NumExpr detected 24 cores but
"NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 16.
2026-06-24 09:30:27,692 - INFO - NumExpr defaulting to 16 threads.
2026-06-24 09:30:28,675 - INFO - No inference_ckpt_path or inference_ckpt_name
provided, selecting default checkpoint.
2026-06-24 09:30:28,676 - INFO - Set diffusion samples to 1
2026-06-24 09:30:28,687 - INFO - Setting RLIMIT_NOFILE to 32768 (was 8192)
2026-06-24 09:30:28,687 - INFO - Setting RLIMIT_STACK to -1 (was 8388608)
2026-06-24 09:30:28,691 - INFO - Loading weights from
/home/rquiroga/.openfold3/params/of3-p2-155k.pt
2026-06-24 09:30:30,648 - INFO - Finished loading weights
2026-06-24 09:30:30,648 - INFO - Loading model state dictionary
2026-06-24 09:31:15,859 - INFO - Finished loading model state dictionary
2026-06-24 09:31:15,899 - INFO - Beginning prediction inference
2026-06-24 09:31:15,900 - INFO - Using bfloat16 Automatic Mixed Precision
(AMP)
2026-06-24 09:31:15,914 - INFO - GPU available: True (cuda), used: True
2026-06-24 09:31:15,914 - INFO - TPU available: False, using: 0 TPU cores
2026-06-24 09:31:15,914 - INFO - 💡 Tip: For seamless cloud logging and
experiment tracking, try installing
[litlogger](https://pypi.org/project/litlogger/) to enable LitLogger, which
logs metrics and artifacts automatically to the Lightning Experiments
platform.
2026-06-24 09:31:15,915 - INFO - 💡 Tip: For seamless cloud uploads and
versioning, try installing [litmodels](https://pypi.org/project/litmodels/) to
enable LitModelCheckpoint, which syncs automatically with the Lightning model
registry.
2026-06-24 09:31:15,916 - INFO - Using output directory: colabfold_msas for
ColabFold MSAs.
2026-06-24 09:31:15,916 - INFO - Submitting 2 sequences to the Colabfold MSA
server for main MSAs...
0%| | 0/300 [elapsed: 00:00 remaining: ?] SUBMIT: 0%| | 0/300 [elapsed: 00:00 remaining: ?] PENDING: 0%| | 0/300 [elapsed: 00:02 remaining: ?]2026-06-24 09:31:18,601 - INFO - Sleeping for 10s. Reason: PENDING
RUNNING: 0%| | 0/300 [elapsed: 00:13 remaining: ?] RUNNING: 3%|▎ | 10/300 [elapsed: 00:13 remaining: 06:36]2026-06-24 09:31:29,597 - INFO - Sleeping for 10s. Reason: RUNNING
RUNNING: 3%|▎ | 10/300 [elapsed: 00:24 remaining: 06:36] RUNNING: 7%|▋ | 20/300 [elapsed: 00:24 remaining: 05:38]2026-06-24 09:31:40,598 - INFO - Sleeping for 9s. Reason: RUNNING
RUNNING: 7%|▋ | 20/300 [elapsed: 00:35 remaining: 05:38] RUNNING: 10%|▉ | 29/300 [elapsed: 00:35 remaining: 05:21]2026-06-24 09:31:51,021 - INFO - Sleeping for 9s. Reason: RUNNING
COMPLETE: 10%|▉ | 29/300 [elapsed: 00:45 remaining: 05:21] COMPLETE: 100%|██████████| 300/300 [elapsed: 00:45 remaining: 00:00] COMPLETE: 100%|██████████| 300/300 [elapsed: 00:47 remaining: 00:00]
2026-06-24 09:32:04,111 - INFO - Submitting 1 paired MSA queries to the
Colabfold MSA server...
Computing paired MSAs: 0%| | 0/1 [00:00<?, ?it/s]
0%| | 0/300 [elapsed: 00:00 remaining: ?][A
SUBMIT: 0%| | 0/300 [elapsed: 00:00 remaining: ?][A
PENDING: 0%| | 0/300 [elapsed: 00:01 remaining: ?][A2026-06-24 09:32:05,122 - INFO - Sleeping for 10s. Reason: PENDING
RUNNING: 0%| | 0/300 [elapsed: 00:12 remaining: ?][A
RUNNING: 3%|▎ | 10/300 [elapsed: 00:12 remaining: 05:49][A2026-06-24 09:32:16,180 - INFO - Sleeping for 7s. Reason: RUNNING
RUNNING: 3%|▎ | 10/300 [elapsed: 00:20 remaining: 05:49][A
RUNNING: 6%|▌ | 17/300 [elapsed: 00:20 remaining: 05:32][A2026-06-24 09:32:24,198 - INFO - Sleeping for 8s. Reason: RUNNING
COMPLETE: 6%|▌ | 17/300 [elapsed: 00:29 remaining: 05:32][A
COMPLETE: 100%|██████████| 300/300 [elapsed: 00:29 remaining: 00:00][A
COMPLETE: 100%|██████████| 300/300 [elapsed: 00:31 remaining: 00:00]
Computing paired MSAs: 100%|██████████| 1/1 [00:31<00:00, 31.19s/it] Computing
paired MSAs: 100%|██████████| 1/1 [00:31<00:00, 31.19s/it]
2026-06-24 09:32:35,301 - INFO - Preprocessing templates for 2 chains
Preprocessing templates: 0%| | 0/2 [00:00<?, ?it/s] Preprocessing templates: 50%|█████ | 1/2 [00:17<00:17, 17.81s/it] Preprocessing templates: 100%|██████████| 2/2 [00:20<00:00, 8.79s/it] Preprocessing templates: 100%|██████████| 2/2 [00:20<00:00, 10.14s/it]
2026-06-24 09:32:55,788 - INFO - Finished preprocessing templates
2026-06-24 09:32:56,086 - INFO - LOCAL_RANK: 0 - CUDA_VISIBLE_DEVICES: [0]
2026-06-24 09:32:56,474 - INFO - Seeding DataModule DatasetMode.prediction
generator with 42
/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/connectors/data_connector.py:434: The
'predict_dataloader' does not have many workers which may be a bottleneck.
Consider increasing the value of the `num_workers` argument` to
`num_workers=23` in the `DataLoader` to improve performance.
Traceback (most recent call last):
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 49, in
_call_and_handle_interrupt
return trainer_fn(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 990, in _predict_impl
results = self._run(model, ckpt_path=ckpt_path, weights_only=weights_only)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 1079, in _run
results = self._run_stage()
^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 1118, in _run_stage
return self.predict_loop.run()
^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/loops/utilities.py", line 179, in _decorator
return loop_run(self, *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/loops/prediction_loop.py", line 105, in run
self.setup_data()
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/loops/prediction_loop.py", line 162, in setup_data
length = len(dl) if has_len_all_ranks(dl, trainer.strategy, allow_zero_length)
else float("inf")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/utilities/data.py", line 105, in has_len_all_ranks
if total_length == 0:
^^^^^^^^^^^^^^^^^
RuntimeError: CUDA error: no kernel image is available for execution on the
device
CUDA kernel errors might be asynchronously reported at some other API call, so
the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1
Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/rquiroga/openfold3/bin/run_openfold", line 8, in <module>
sys.exit(cli())
^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/click/core.py", line
1524, in __call__
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/click/core.py", line
1445, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/click/core.py", line
1912, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/click/core.py", line
1308, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-packages/click/core.py", line
877, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/openfold3/run_openfold.py", line 257, in predict
expt_runner.run(query_set)
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/openfold3/entry_points/experiment_runner.py", line 704, in run
self.trainer.predict(
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 941, in predict
return call._call_and_handle_interrupt(
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/call.py", line 70, in
_call_and_handle_interrupt
trainer._teardown()
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/trainer/trainer.py", line 1102, in _teardown
self.strategy.teardown()
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/pytorch_lightning/strategies/strategy.py", line 536, in teardown
self.lightning_module.cpu()
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/lightning_fabric/utilities/device_dtype_mixin.py", line 86, in cpu
return super().cpu()
^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 1133, in cpu
return self._apply(lambda t: t.cpu())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 915, in _apply
module._apply(fn)
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/torch/nn/modules/module.py", line 915, in _apply
module._apply(fn)
File "/home/rquiroga/openfold3/lib/python3.11/site-
packages/torchmetrics/metric.py", line 907, in _apply
_dummy_tensor = fn(torch.zeros(1, device=self.device))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
RuntimeError: CUDA error: no kernel image is available for execution on the
device
CUDA kernel errors might be asynchronously reported at some other API call, so
the stacktrace below might be incorrect.
For debugging consider passing CUDA_LAUNCH_BLOCKING=1
Compile with `TORCH_USE_CUDA_DSA` to enable device-side assertions.
> rename #2 1m27-
> openfold predict protein #2/A name 1m27_A_F77I device cpu
Running OpenFold prediction of protein with 104 residues on cpu
Using multiple sequence alignment server https://api.colabfold.com
> rename #2 1m27_F77I
Confidence pTM 0.76, , pLDDT 82
OpenFold prediction completed in 163 seconds (start openfold 5 sec, initialize
neural net 46 sec, sequence search 35 sec, structure inference 66 sec)
Please cite OpenFold-1 Democratizing Biomolecular Interaction Modeling.
BioRxiv https://doi.org/10.1101/2024.11.19.624167 if you use these
predictions.
> open
> /home/rquiroga/Desktop/openfold/1m27_A_F77I_1/1m27_A_F77I/seed_42/1m27_A_F77I_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1m27_F77I, chain A (#2) with
1m27_A_F77I_seed_42_sample_1_model.cif, chain A (#5), sequence alignment score
= 522.6
RMSD between 95 pruned atom pairs is 0.574 angstroms; (across all 104 pairs:
1.400)
> save /home/rquiroga/colaboraciones/Eva/openfold.cxs
> select #5/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> openfold predict protein #1/A protein #1/B protein #1/C name 1m27_A_F77I
> device cpu
Running OpenFold prediction of 3 proteins with 176 residues on cpu
Using multiple sequence alignment server https://api.colabfold.com
> hide #2 models
> show #1 models
> select #1/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
Confidence pTM 0.64, ipTM 0.49, pLDDT 82
OpenFold prediction completed in 259 seconds (start openfold 5 sec, initialize
neural net 49 sec, sequence search 35 sec, structure inference 142 sec)
> open
> /home/rquiroga/Desktop/openfold/1m27_A_F77I_2/1m27_A_F77I/seed_42/1m27_A_F77I_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1m27, chain A (#1) with 1m27_A_F77I_seed_42_sample_1_model.cif,
chain A (#6), sequence alignment score = 521
RMSD between 102 pruned atom pairs is 0.412 angstroms; (across all 104 pairs:
0.836)
> hide #3 models
> hide #4 models
> hide #1 models
> rename #2 1m27_A_F77I
> open 1m27
1m27 title:
Crystal structure of SAP/FynSH3/SLAM ternary complex [more info...]
Chain information for 1m27 #7
---
Chain | Description | UniProt
A | SH2 domain protein 1A | SH21A_HUMAN 1-104
B | Signaling lymphocytic activation molecule | SLAF1_HUMAN 276-286
C | Proto-oncogene tyrosine-protein kinase FYN | FYN_HUMAN 84-144
Non-standard residues in 1m27 #7
---
FLC — citrate anion
> hide #5 models
> hide #6 models
> select #7/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ILE rotLib Dynameomics
1m27 #7/A PHE 77: phi -144.4, psi 135.0 trans
Changed 45 bond radii
> clashes #!7 & ~#!7/A:77 & ~solvent overlapCutoff 0.4 radius 0.075 reveal
> true restrict #7.1 & ~@c,ca,n
45 clashes
> swapaa #!7/A:77 ILE criteria 7 rotLib Dynameomics
Using Dynameomics library
1m27 #!7/A PHE 77: phi -144.4, psi 135.0 trans
Applying ILE rotamer (chi angles: -61.2 101.7) to 1m27 #!7/A ILE 77
> show sel atoms
> select clear
> select #7/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> rename #7 1m27_F77I
> openfold predict protein #1/A protein #1/B protein #1/C name
> 1m27_F77I_complex device cpu
Running OpenFold prediction of 3 proteins with 176 residues on cpu
Using cached multiple sequence alignment
/home/rquiroga/Downloads/ChimeraX/OpenFoldMSA/1m27_A_F77I_1
> rename #5 OF3_1m27_A_F77I.cif
> rename #6 OF3_1m27.cif
> show #6 models
> hide #7 models
> show #5 models
> select #6/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> color bfactor sel
11 atoms, 1 residues, atom bfactor range 76.1 to 82.6
Confidence pTM 0.63, ipTM 0.50, pLDDT 82
OpenFold prediction completed in 201 seconds (start openfold 5 sec, initialize
neural net 45 sec, sequence search 0 sec, structure inference 144 sec)
> open
> /home/rquiroga/Desktop/openfold/1m27_F77I_complex/1m27_F77I_complex/seed_42/1m27_F77I_complex_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1m27, chain A (#1) with
1m27_F77I_complex_seed_42_sample_1_model.cif, chain A (#8), sequence alignment
score = 521
RMSD between 102 pruned atom pairs is 0.399 angstroms; (across all 104 pairs:
0.815)
> interfaces select & ~solvent
Missing or invalid "atoms" argument: invalid atoms specifier
> hide #6 models
> hide #5 models
> select #8/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> rename #8 OF3_1m27_F77I_complex.cif
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> show #6 models
> hide #8 models
> show #1 models
> show #8 models
> hide #8 models
> hide #6 models
> show #6 models
> hide #6 models
> show #8 models
> select clear
> select #1/C:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select #8/C:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #8 models
> show #8 models
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> hide #8 models
> show #5 models
> hide #5 models
> show #6 models
> show #8 models
> hide #8 models
> close #8
> hide #6 models
> show #7 models
> hide #1 models
> openfold predict protein #1/B protein #1/C protein #7/A name
> 1m27_F77I_complex device cpu
Running OpenFold prediction of 3 proteins with 176 residues on cpu
Using multiple sequence alignment server https://api.colabfold.com
> show #6 models
> show #5 models
> hide #5 models
> hide #6 models
> show #5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict both interModel false ignoreHiddenModels true reveal
> true
No contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true reveal
> true
12 contacts
> select clear
> hide #!5 models
> show #6 models
> select #6/A:77@CE1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true reveal
> true
29 contacts
> hide #7 models
> hide #!6 models
> show #1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true reveal
> true
26 contacts
> select clear
> hide #!1 models
> show #!5 models
> show #!6 models
> hide #!5 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/A:77@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select subtract #6/A:77@O
10 atoms, 10 bonds, 1 residue, 1 model selected
> select subtract #6/A:77@C
9 atoms, 9 bonds, 1 residue, 1 model selected
> select subtract #6/A:77@N
8 atoms, 8 bonds, 1 residue, 1 model selected
> select subtract #6/A:77@CA
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> show #!1 models
> open 1m27
1m27 title:
Crystal structure of SAP/FynSH3/SLAM ternary complex [more info...]
Chain information for 1m27 #8
---
Chain | Description | UniProt
A | SH2 domain protein 1A | SH21A_HUMAN 1-104
B | Signaling lymphocytic activation molecule | SLAF1_HUMAN 276-286
C | Proto-oncogene tyrosine-protein kinase FYN | FYN_HUMAN 84-144
Non-standard residues in 1m27 #8
---
FLC — citrate anion
> rename #8 1m27_A
> hide #6.1 models
> hide #!6 models
> select clear
> select #1/C:99
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #1/B:281
20 atoms, 19 bonds, 2 residues, 1 model selected
> select up
186 atoms, 189 bonds, 22 residues, 1 model selected
> select up
582 atoms, 595 bonds, 72 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> hide #!1 models
> show #!1 models
> rename #1 1m27_A
> rename #8 1m27
> hide #8 models
> select #1/A:77@CB
1 atom, 1 residue, 1 model selected
> select add #1/A:77@CG
2 atoms, 1 residue, 1 model selected
> select add #1/A:77@CD2
3 atoms, 1 residue, 1 model selected
> select add #1/A:77@CE2
4 atoms, 1 residue, 1 model selected
> select add #1/A:77@CZ
5 atoms, 1 residue, 1 model selected
> select add #1/A:77@CE1
6 atoms, 1 residue, 1 model selected
> select add #1/A:77@CD1
7 atoms, 1 residue, 1 model selected
Confidence pTM 0.66, ipTM 0.50, pLDDT 81
OpenFold prediction completed in 327 seconds (start openfold 6 sec, initialize
neural net 47 sec, sequence search 117 sec, structure inference 141 sec)
> open
> /home/rquiroga/Desktop/openfold/1m27_F77I_complex_1/1m27_F77I_complex/seed_42/1m27_F77I_complex_seed_42_sample_1_model.cif
> logInfo false
> contacts sel restrict cross interModel false ignoreHiddenModels true reveal
> true
15 contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true reveal
> true
15 contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.045 reveal true
15 contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.035 reveal true
15 contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
15 contacts
> select #1/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #1/A:77@CE2
1 atom, 1 residue, 1 model selected
> select add #1/A:77@CZ
2 atoms, 1 residue, 1 model selected
> select add #1/A:77@CD2
3 atoms, 1 residue, 1 model selected
> select add #1/A:77@CG
4 atoms, 1 residue, 1 model selected
> select add #1/A:77@CD1
5 atoms, 1 residue, 1 model selected
> select add #1/A:77@CE1
6 atoms, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
15 contacts
> select add #1/A:77@CB
7 atoms, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
15 contacts
> hide #!1 models
> hide #9 models
> show #9 models
> select clear
> show #8 models
> hide #8 models
> show #8 models
> show #!6 models
> hide #!6 models
> ui tool show Matchmaker
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27_A, chain A (#1) with
1m27_F77I_complex_seed_42_sample_1_model.cif, chain A (#9), sequence alignment
score = 520.4
RMSD between 95 pruned atom pairs is 0.644 angstroms; (across all 104 pairs:
1.392)
> matchmaker #9 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27_A, chain A (#1) with
1m27_F77I_complex_seed_42_sample_1_model.cif, chain A (#9), sequence alignment
score = 520.4
RMSD between 95 pruned atom pairs is 0.644 angstroms; (across all 104 pairs:
1.392)
> hide #9 models
> show #9 models
> hide #9 models
> show #9 models
> hide #8 models
> select #9/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> rename #9 OF3_1m27_F77I_complex.cif
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #9 models
> show #!5 models
> select #5/A:77@CG2
1 atom, 1 residue, 1 model selected
> select add #5/A:77@CB
2 atoms, 1 residue, 1 model selected
> select subtract #5/A:77@CB
1 atom, 1 residue, 1 model selected
> select add #5/A:77@CG1
2 atoms, 1 residue, 1 model selected
> select add #5/A:77@CD1
3 atoms, 1 bond, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
7 contacts
> hide #!5 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #8 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
59 atoms, 62 bonds, 6 residues, 1 model selected
> select up
491 atoms, 504 bonds, 61 residues, 1 model selected
> select up
1404 atoms, 1437 bonds, 176 residues, 1 model selected
> select down
491 atoms, 504 bonds, 61 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select add #6/A:77@CD1
3 atoms, 2 bonds, 1 residue, 1 model selected
> select add #6/A:77@CG
4 atoms, 3 bonds, 1 residue, 1 model selected
> select add #6/A:77@CD2
5 atoms, 4 bonds, 1 residue, 1 model selected
> select add #6/A:77@CE2
6 atoms, 5 bonds, 1 residue, 1 model selected
> select add #6/A:77@CB
7 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
14 contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
14 contacts
> hide #8 models
> show #6.1 models
> show #9 models
> hide #9 models
> show #!5 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #8 models
> hide #!5 models
> hide #!6 models
> hide #6.1 models
> select #8/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/A:79
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> select #8/C:100
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #8/C:99
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #8/C:98
25 atoms, 22 bonds, 3 residues, 1 model selected
> select add #8/C:97
32 atoms, 28 bonds, 4 residues, 1 model selected
> show sel atoms
> select #8/A:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #8/A:78
22 atoms, 20 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!5 models
> hide #!5 models
> show #!5 models
> select #5/A:78
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #5/A:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!6 models
> show #!6 models
> hide #!5 models
> select #6/A:78
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #8 models
> show #6.1 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel cartoons
> hide #!6 models
> show #!5 models
> select #5/A:75@CZ
1 atom, 1 residue, 1 model selected
> select add #5/A:63@CB
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
4 atoms, 1 bond, 3 residues, 1 model selected
> select up
28 atoms, 25 bonds, 3 residues, 1 model selected
> hide sel atoms
> hide #!5 models
> show #!6 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #!5 models
> show #!1 models
> hide #!1 models
> hide #!5 models
> hide #5.1 models
> show #!5 models
> show #5.1 models
> show #!1 models
> hide #!5 models
> hide #5.1 models
> hide #!6 models
> hide #6.1 models
> hide #1.1 models
> show #8 models
> show #9 models
> hide #8 models
> show #!5 models
> hide #!5 models
> hide #!1 models
> show #!1 models
> hide #!1 models
> show #8 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #!5 models
> hide #!5 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #9 models
> open 1d4w
1d4w title:
Crystal structure of the XLP protein sap In complex with slam phosphopeptide
[more info...]
Chain information for 1d4w #10
---
Chain | Description | UniProt
A B | T CELL SIGNAL TRANSDUCTION MOLECULE SAP | SH21A_HUMAN 1-104
C D | SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE | SLAF1_HUMAN 276-286
1d4w mmCIF Assemblies
---
1| software_defined_assembly
2| software_defined_assembly
> open 1d4t
1d4t title:
Crystal structure of the XLP protein sap In complex with A slam peptide [more
info...]
Chain information for 1d4t #11
---
Chain | Description | UniProt
A | T CELL SIGNAL TRANSDUCTION MOLECULE SAP | SH21A_HUMAN 1-104
B | SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE | SLAF1_HUMAN 276-286
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1071 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> ui tool show Matchmaker
> matchmaker #10-11 to #8
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#8) with 1d4w, chain A (#10), sequence alignment
score = 521
RMSD between 98 pruned atom pairs is 0.519 angstroms; (across all 104 pairs:
1.069)
Matchmaker 1m27, chain A (#8) with 1d4t, chain A (#11), sequence alignment
score = 521
RMSD between 101 pruned atom pairs is 0.506 angstroms; (across all 104 pairs:
0.971)
> select clear
> hide #8 models
> hide #11 models
> show #11 models
> hide #10 models
> show #10 models
> matchmaker #10/B to #1/A pairing ss
Parameters
---
Chain pairing | ss
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27_A, chain A (#1) with 1d4w, chain B (#10), sequence alignment
score = 518.6
RMSD between 100 pruned atom pairs is 0.475 angstroms; (across all 102 pairs:
0.598)
> select clear
> select #10/A:85
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
81 atoms, 81 bonds, 10 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> select up
1017 atoms, 845 bonds, 296 residues, 1 model selected
> select up
2203 atoms, 1830 bonds, 639 residues, 1 model selected
> select down
1017 atoms, 845 bonds, 296 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> select clear
[Repeated 1 time(s)]Drag select of 3 residues
> select up
85 atoms, 85 bonds, 10 residues, 1 model selected
> delete atoms sel
> delete bonds sel
> show #8 models
> open 1d4t
1d4t title:
Crystal structure of the XLP protein sap In complex with A slam peptide [more
info...]
Chain information for 1d4t #12
---
Chain | Description | UniProt
A | T CELL SIGNAL TRANSDUCTION MOLECULE SAP | SH21A_HUMAN 1-104
B | SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE | SLAF1_HUMAN 276-286
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1071 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> rename #12 1d4t_F77I
> hide #8 models
> hide #10 models
> hide #11 models
> ui tool show Matchmaker
> matchmaker #12 to #1
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27_A, chain A (#1) with 1d4t_F77I, chain A (#12), sequence
alignment score = 521
RMSD between 101 pruned atom pairs is 0.506 angstroms; (across all 104 pairs:
0.971)
> show #11 models
> hide #11 models
> select clear
> select #12/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Rotamers
> swapaa interactive sel ILE rotLib Dynameomics
1d4t_F77I #12/A PHE 77: phi -124.9, psi 142.6 trans
Changed 45 bond radii
> clashes #!12 & ~#!12/A:77 & ~solvent overlapCutoff 0.4 radius 0.075 reveal
> true restrict #12.1 & ~@c,ca,n
62 clashes
> swapaa #!12/A:77 ILE criteria 6 rotLib Dynameomics
Using Dynameomics library
1d4t_F77I #!12/A PHE 77: phi -124.9, psi 142.6 trans
Applying ILE rotamer (chi angles: 59.3 95.4) to 1d4t_F77I #!12/A ILE 77
> show sel atoms
> select #12/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
100 atoms, 102 bonds, 12 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> ui tool show OpenFold
> openfold predict protein #12/A name 1d4t_F77I_complex device cpu
Running OpenFold prediction of protein with 104 residues on cpu
Using cached multiple sequence alignment
/home/rquiroga/Downloads/ChimeraX/OpenFoldMSA/1m27_A_F77I_0
Confidence pTM 0.76, , pLDDT 82
OpenFold prediction completed in 116 seconds (start openfold 5 sec, initialize
neural net 45 sec, sequence search 0 sec, structure inference 59 sec)
> open
> /home/rquiroga/Desktop/openfold/1d4t_F77I_complex/1d4t_F77I_complex/seed_42/1d4t_F77I_complex_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1d4t_F77I, chain A (#12) with
1d4t_F77I_complex_seed_42_sample_1_model.cif, chain A (#13), sequence
alignment score = 529.8
RMSD between 99 pruned atom pairs is 0.621 angstroms; (across all 104 pairs:
1.201)
> rename #13 1d4t_F77I
> hide #13 models
> rename #13 OF3_1d4t_F77I_complex
> show #13 models
> hide #12 models
> show #12 models
> rename #13 OF3_1d4t_F77I
> openfold predict protein #11/A name 1d4t_wt device cpu
Running OpenFold prediction of protein with 104 residues on cpu
Using multiple sequence alignment server https://api.colabfold.com
Confidence pTM 0.80, , pLDDT 85
OpenFold prediction completed in 140 seconds (start openfold 5 sec, initialize
neural net 49 sec, sequence search 0 sec, structure inference 60 sec)
> open
> /home/rquiroga/Desktop/openfold/1d4t_wt/1d4t_wt/seed_42/1d4t_wt_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1d4t, chain A (#11) with 1d4t_wt_seed_42_sample_1_model.cif, chain
A (#14), sequence alignment score = 534.8
RMSD between 99 pruned atom pairs is 0.622 angstroms; (across all 104 pairs:
1.171)
> rename #14 OF3_1d4t_wt.cif
> hide #13 models
> show #13 models
> hide #13 models
> hide #12 models
> hide #14 models
> openfold predict protein #11/A protein #11/B name OF3_1d4t_wt_complex device
> cpu
Running OpenFold prediction of 2 proteins with 115 residues on cpu
Using multiple sequence alignment server https://api.colabfold.com
Confidence pTM 0.89, ipTM 0.75, pLDDT 90
OpenFold prediction completed in 163 seconds (start openfold 5 sec, initialize
neural net 50 sec, sequence search 26 sec, structure inference 71 sec)
> open
> /home/rquiroga/Desktop/openfold/OF3_1d4t_wt_complex/OF3_1d4t_wt_complex/seed_42/OF3_1d4t_wt_complex_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1d4t, chain A (#11) with
OF3_1d4t_wt_complex_seed_42_sample_1_model.cif, chain A (#15), sequence
alignment score = 534.8
RMSD between 104 pruned atom pairs is 0.534 angstroms; (across all 104 pairs:
0.534)
> rename #15 OF3_1d4t_wt_complex
> show #14 models
> hide #14 models
> openfold predict protein #12/A protein #12/B name OF3_1d4t_F77I_complex
> device cpu
Running OpenFold prediction of 2 proteins with 115 residues on cpu
Using multiple sequence alignment server https://api.colabfold.com
> show #14 models
> hide #14 models
> show #13 models
> hide #13 models
> close #6
> close #5
> show #9 models
> hide #9 models
> show #9 models
> hide #9 models
> close #13-14
> rename #7 id #5
> rename #8 id #6
> rename #9 id #7
> rename #10 id #8
> rename #11 id #9
> rename #12 id #10
> rename #15 id #11
> close #3
> close #4
Confidence pTM 0.87, ipTM 0.75, pLDDT 88
OpenFold prediction completed in 179 seconds (start openfold 5 sec, initialize
neural net 47 sec, sequence search 46 sec, structure inference 68 sec)
> open
> /home/rquiroga/Desktop/openfold/OF3_1d4t_F77I_complex/OF3_1d4t_F77I_complex/seed_42/OF3_1d4t_F77I_complex_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1d4t_F77I, chain A (#10) with
OF3_1d4t_F77I_complex_seed_42_sample_1_model.cif, chain A (#3), sequence
alignment score = 533.4
RMSD between 104 pruned atom pairs is 0.498 angstroms; (across all 104 pairs:
0.498)
> rename #3 id #12
> hide #11 models
> show #11 models
> hide #12 models
> show #12 models
> show #7 models
> hide #7 models
> show #7 models
> hide #7 models
> log metadata #11
The model has no metadata
> log chains #11
Chain information for OF3_1d4t_wt_complex #11
---
Chain | Description
A | No description available
B | No description available
> rename #12 OF3_1d4t_F77I_complex.cif
> show #7 models
> hide #11 models
> hide #12 models
> show #12 models
> hide #12 models
> show #12 models
> ui tool show OpenFold
> openfold predict protein #6/A protein #6/B name OF3_1m27_wt_complex device
> cpu
Running OpenFold prediction of 2 proteins with 115 residues on cpu
Using cached multiple sequence alignment
/home/rquiroga/Downloads/ChimeraX/OpenFoldMSA/OF3_1d4t_wt_complex
Confidence pTM 0.89, ipTM 0.75, pLDDT 90
OpenFold prediction completed in 130 seconds (start openfold 5 sec, initialize
neural net 45 sec, sequence search 0 sec, structure inference 73 sec)
> open
> /home/rquiroga/Desktop/openfold/OF3_1m27_wt_complex/OF3_1m27_wt_complex/seed_42/OF3_1m27_wt_complex_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1m27, chain A (#6) with
OF3_1m27_wt_complex_seed_42_sample_1_model.cif, chain A (#3), sequence
alignment score = 521
RMSD between 101 pruned atom pairs is 0.476 angstroms; (across all 104 pairs:
0.917)
> rename #3 OF3_1m27_wt_complex
> rename #5 id #4
> select add #6
1506 atoms, 1452 bonds, 263 residues, 1 model selected
> rename #6 id #5
> select subtract #5
Nothing selected
> rename #7 id #6
> rename #3 id #7
> hide #12 models
> hide #6 models
> show #6 models
> hide #7 models
> hide #6 models
> show #7 models
> show #6 models
> hide #7 models
> show #7 models
> hide #6 models
> show #6 models
> hide #7 models
> show #7 models
> hide #6 models
> open 1d4t
1d4t title:
Crystal structure of the XLP protein sap In complex with A slam peptide [more
info...]
Chain information for 1d4t #3
---
Chain | Description | UniProt
A | T CELL SIGNAL TRANSDUCTION MOLECULE SAP | SH21A_HUMAN 1-104
B | SIGNALING LYMPHOCYTIC ACTIVATION MOLECULE | SLAF1_HUMAN 276-286
35 atoms have alternate locations. Control/examine alternate locations with
Altloc Explorer [start tool...] or the altlocs command.
1071 atoms have anisotropic B-factors. Depict anisotropic information with
Thermal Ellipsoids [start tool...] or the aniso command.
> hide #3 models
> show #5 models
> hide #7 models
> select #5/B:279
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> color sel red
> select #5/C:131
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 5 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> color sel orange
> color sel lime
> select clear
> select #5/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel target ab
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sap_slam_fyn_wt/fold_sap_slam_fyn_model_0.cif
Chain information for fold_sap_slam_fyn_model_0.cif #13
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #13 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sap_slam_fyn_model_0.cif, chain A
(#13), sequence alignment score = 524.6
RMSD between 102 pruned atom pairs is 0.384 angstroms; (across all 104 pairs:
0.746)
> select #13/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #13/C:16
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> select #13/A:78
11 atoms, 10 bonds, 1 residue, 1 model selected
> hide #5 models
> select #13/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> select up
1407 atoms, 1440 bonds, 176 residues, 1 model selected
> color bfactor #13 palette alphafold
1407 atoms, 176 residues, atom bfactor range 55.1 to 98.9
> select clear
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sapf77i_slam_fyn_wt/fold_sap_f77i_slam_fyn_model_0.cif
Chain information for fold_sap_f77i_slam_fyn_model_0.cif #14
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> ui tool show Matchmaker
> matchmaker #14 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sap_f77i_slam_fyn_model_0.cif, chain A
(#14), sequence alignment score = 520.4
RMSD between 101 pruned atom pairs is 0.465 angstroms; (across all 104 pairs:
0.869)
> matchmaker #14 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sap_f77i_slam_fyn_model_0.cif, chain A
(#14), sequence alignment score = 520.4
RMSD between 101 pruned atom pairs is 0.465 angstroms; (across all 104 pairs:
0.869)
> color bfactor #14 palette alphafold
1404 atoms, 176 residues, atom bfactor range 55.2 to 98.9
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> hide #14 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #13 models
> hide #13 models
> show #14 models
> hide #14 models
> show #13 models
> hide #13 models
> show #14 models
> show #13 models
> hide #14 models
> hide #13 models
> show #14 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> hide #13 models
> show #13 models
> select #14/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #14/C:16
17 atoms, 15 bonds, 2 residues, 1 model selected
> show sel atoms
> select #13/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #14/A:82
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel cartoons
> show sel atoms
> select #13/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> select #14/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #13 models
> hide #14 models
> rename #13 AF3_sap_slam_fyn_model_0.cif
> rename #14 AF3_sap_f77i_slam_fyn_model_0.cif
> show #11 models
> show #12 models
> hide #11 models
> hide #12 models
> show #6 models
> show #7 models
> show #2 models
> show #4 models
> hide #4 models
> hide #2 models
> close #2
> hide #6 models
> hide #7 models
> show #7 models
> rename #7 OF3_1m27_wt_SAP_SLAM
> openfold predict protein #4/A protein #4/B name OF3_1m27_F77I_SAP_SLAM
> device cpu
Running OpenFold prediction of 2 proteins with 115 residues on cpu
Using cached multiple sequence alignment
/home/rquiroga/Downloads/ChimeraX/OpenFoldMSA/OF3_1d4t_F77I_complex
> hide #7 models
> show #6 models
> rename #6 OF3_1m27_F77I_SAP_SLAM_FYN
> show #7 models
> hide #6 models
Confidence pTM 0.87, ipTM 0.74, pLDDT 88
OpenFold prediction completed in 127 seconds (start openfold 6 sec, initialize
neural net 45 sec, sequence search 0 sec, structure inference 70 sec)
> open
> /home/rquiroga/Desktop/openfold/OF3_1m27_F77I_SAP_SLAM/OF3_1m27_F77I_SAP_SLAM/seed_42/OF3_1m27_F77I_SAP_SLAM_seed_42_sample_1_model.cif
> logInfo false
Matchmaker 1m27_F77I, chain A (#4) with
OF3_1m27_F77I_SAP_SLAM_seed_42_sample_1_model.cif, chain A (#2), sequence
alignment score = 519.6
RMSD between 102 pruned atom pairs is 0.519 angstroms; (across all 104 pairs:
0.901)
> rename #2 OF3_1m27_F77I_SAP_SLAM
> rename #14 id #15
> rename #13 id #14
> rename #12 id #13
> rename #11 id #12
> rename #10 id #11
> rename #9 id #10
> rename #8 id #9
> rename #2 id #8
> show #6 models
> hide #6 models
> show #6 models
> hide #6 models
> close #6
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #7 models
> show #7 models
> hide #8 models
> show #8 models
> hide #8 models
> show #8 models
> hide #7 models
> show #7 models
> hide #7 models
> show #7 models
> hide #8 models
> hide #7 models
> show #7 models
> show #8 models
> hide #8 models
> hide #7 models
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sap_slam_wt/fold_sap_f77i_slam_model_0.cif
Chain information for fold_sap_f77i_slam_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sapf77i_slam/fold_sapwt_slam_model_0.cif
Chain information for fold_sapwt_slam_model_0.cif #6
---
Chain | Description
A | .
B | .
Computing secondary structure
> hide #2 models
> hide #6 models
> rename #6 id #16
> rename #2 id #17
> rename #16 AF3_sapwt_slam_model_0.cif
> rename #17 AF3_sap_f77i_slam_model_0.cif
> ui tool show Matchmaker
> matchmaker #16-17 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with AF3_sapwt_slam_model_0.cif, chain A (#16),
sequence alignment score = 524.6
RMSD between 102 pruned atom pairs is 0.417 angstroms; (across all 104 pairs:
0.868)
Matchmaker 1m27, chain A (#5) with AF3_sap_f77i_slam_model_0.cif, chain A
(#17), sequence alignment score = 520.4
RMSD between 101 pruned atom pairs is 0.435 angstroms; (across all 104 pairs:
0.885)
> show #16 models
> show #17 models
> color bfactor #16 palette alphafold
915 atoms, 115 residues, atom bfactor range 51.5 to 99
> color bfactor #17 palette alphafold
912 atoms, 115 residues, atom bfactor range 51.8 to 99
> hide #17 models
> hide #16 models
> show #17 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> show #16 models
> hide #16 models
> close #16
> close #17
> open
> /home/rquiroga/colaboraciones/Eva/fold_sapwt_slam/fold_sapwt_slam_model_0.cif
Chain information for fold_sapwt_slam_model_0.cif #2
---
Chain | Description
A | .
B | .
Computing secondary structure
> open
> /home/rquiroga/colaboraciones/Eva/fold_sap_f77i_slam/fold_sap_f77i_slam_model_0.cif
Chain information for fold_sap_f77i_slam_model_0.cif #6
---
Chain | Description
A | .
B | .
Computing secondary structure
> rename #2 id #16
> rename #6 id #17
> ui tool show Matchmaker
> matchmaker #16-17 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sapwt_slam_model_0.cif, chain A (#16),
sequence alignment score = 524.6
RMSD between 102 pruned atom pairs is 0.417 angstroms; (across all 104 pairs:
0.868)
Matchmaker 1m27, chain A (#5) with fold_sap_f77i_slam_model_0.cif, chain A
(#17), sequence alignment score = 520.4
RMSD between 101 pruned atom pairs is 0.435 angstroms; (across all 104 pairs:
0.885)
> matchmaker #16-17 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sapwt_slam_model_0.cif, chain A (#16),
sequence alignment score = 524.6
RMSD between 102 pruned atom pairs is 0.417 angstroms; (across all 104 pairs:
0.868)
Matchmaker 1m27, chain A (#5) with fold_sap_f77i_slam_model_0.cif, chain A
(#17), sequence alignment score = 520.4
RMSD between 101 pruned atom pairs is 0.435 angstroms; (across all 104 pairs:
0.885)
> color bfactor #17 palette alphafold
912 atoms, 115 residues, atom bfactor range 51.8 to 99
> color bfactor #16 palette alphafold
915 atoms, 115 residues, atom bfactor range 51.5 to 99
> hide #17 models
> show #17 models
> hide #16 models
> show #16 models
> hide #17 models
> show #17 models
> hide #16 models
> show #16 models
> hide #17 models
> show #17 models
> hide #16 models
> select #17/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
Cannot increment value
> show #16 models
> hide #17 models
> select clear
> select #16/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> show sel atoms
> show #17 models
> select clear
> select #17/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #16/A:82
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
> hide #17 models
> show #17 models
> hide #16 models
> show #16 models
> hide #17 models
> show #17 models
> hide #17 models
> show #17 models
> hide sel atoms
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
20 contacts
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
12 contacts
> hide #!17 models
> hide #!16 models
> show #!17 models
> hide #16.1 models
> hide #!17 models
> show #!16 models
> show #16.1 models
> select #16/A:77@CB
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
15 contacts
> hide #!16 models
> show #!17 models
> select #17/A:77@CB
1 atom, 1 residue, 1 model selected
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
7 contacts
> select clear
> show #!16 models
> hide #!16 models
> hide #16.1 models
> show #!16 models
> show #16.1 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> select #16/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> select down
47 atoms, 46 bonds, 6 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select clear
> hide #!16 models
> hide #16.1 models
> hide #!17 models
> show #!16 models
> show #5 models
> hide #!16 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> show #!1 models
> show #1.1 models
> hide #5 models
> hide #!1 models
> hide #1.1 models
> show #5 models
> show #13 models
> hide #5 models
> show #12 models
> hide #12 models
> hide #13 models
> show #14 models
> show #15 models
> show #5 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
103 atoms, 106 bonds, 12 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> select up
890 atoms, 857 bonds, 157 residues, 1 model selected
> select up
1506 atoms, 1452 bonds, 263 residues, 1 model selected
> select down
890 atoms, 857 bonds, 157 residues, 1 model selected
> show sel surfaces
> hide #5.1 models
> hide #14 models
> hide #15 models
> select #5/A:77@CB
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> color (#!5 & sel) red
> show #5.1 models
> hide #5.1 models
> show #5.1 models
> hide #5.1 models
> show #!1 models
> hide #!1 models
> show #4 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
100 atoms, 102 bonds, 12 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel red
> show sel surfaces
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
72 atoms, 72 bonds, 9 residues, 2 models selected
> select up
822 atoms, 841 bonds, 104 residues, 2 models selected
> show sel surfaces
> hide #4.1 models
> select #4/A:76
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
100 atoms, 102 bonds, 12 residues, 2 models selected
> select up
822 atoms, 841 bonds, 104 residues, 2 models selected
> select up
887 atoms, 853 bonds, 157 residues, 2 models selected
> select up
1503 atoms, 1448 bonds, 263 residues, 2 models selected
> select down
887 atoms, 853 bonds, 157 residues, 2 models selected
> show sel surfaces
> hide #!5 models
> hide #4.1 models
> select #4/A:77@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select up
100 atoms, 102 bonds, 12 residues, 2 models selected
> select down
8 atoms, 7 bonds, 1 residue, 2 models selected
> color (#!4 & sel) red
> show #4.1 models
> select #4/C:98
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> hide #!4 models
> show #!5 models
> show #5.1 models
> show #!4 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!5 models
> show #!5 models
> hide #!4 models
> show #!4 models
> hide #!4 models
> hide #!5 models
> show #!16 models
> show #!17 models
> select #17/A:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #16/A:82
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel cartoons
[Repeated 1 time(s)]
> show sel atoms
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> show #16.1 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!17 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> rename #16 AF3_sapwt_slam_model_0.cif
> rename #17 AF3_sap_f77i_slam_model_0.cif
> show #!17 models
> show #!16 models
> hide #!16 models
> show #!16 models
> colorkey show true
Unknown command: colorkey show true
> ui tool show "Render/Select by Attribute"
Fetching compressed palette bands from
https://www.colourlovers.com/api/palettes?keywords=bands&format=json&numResults=100
> key alphafold bands 5
Expected a keyword
> key alphafold
> key alphafold fontSize 16 labelSide top
Invalid "labelSide" argument: Should be one of 'left/top' or 'right/bottom'
> key alphafold fontSize 16
> key "blue:Very high (>90)" "cornflower blue:Confident (70-90)" "yellow:Low
> (50-70)" "orange:Very low (<50)" bands 4
Expected a keyword
> key alphafold bands 4 "blue:Very high (>90)" "cornflower blue:Confident
> (70-90)" "yellow:Low (50-70)" "orange:Very low (<50)"
Expected a keyword
> key alphafold"blue:Very high (>90)"" "cornflower blue:Confident (70-90)"
> "yellow:Low (50-70)" "orange:Very low (<50)"
> key alphafold"blue:>90"" "cornflower blue:70-90" "yellow:50-70" "orange:<50"
> key alphafold fontSize 16
> hide #!16 models
> hide #!17 models
> show #14 models
> show #15 models
> hide #15 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true radius 0.025 reveal true
6 contacts
> hide #!14 models
> show #15 models
> select #15/A:77@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true radius 0.025 reveal true
5 contacts
> hide #!15 models
> show #!14 models
> select #14/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> show sel atoms
> show sel cartoons
> select clear
Fetching compressed palette remove from
https://www.colourlovers.com/api/palettes?keywords=remove&format=json&numResults=100
> key remove
Fetching compressed palette none from
https://www.colourlovers.com/api/palettes?keywords=none&format=json&numResults=100
Found 2 ColourLover palettes with name "none", using palette id 2581993 by
author lavender_mint with most views (81). To choose a different one use "name
by author" or id number.
> key none
> key
> key delete
> select up
6 atoms, 6 bonds, 1 residue, 1 model selected
> select down
6 bonds, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true radius 0.025 reveal true
3 contacts
> hide #!14 models
> show #!15 models
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true radius 0.025 reveal true
3 contacts
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!15 models
> show #!14 models
> hide #!15 models
> hide #!14 models
> show #!16 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> show #!14 models
> hide #!14 models
> hide #!16 models
> show #!15 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> ui tool show Matchmaker
> matchmaker #!16 to #14
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
AF3_sapwt_slam_model_0.cif, chain A (#16), sequence alignment score = 535.4
RMSD between 104 pruned atom pairs is 0.203 angstroms; (across all 104 pairs:
0.203)
> matchmaker #!17 to #15
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF3_sap_f77i_slam_fyn_model_0.cif, chain A (#15) with
AF3_sap_f77i_slam_model_0.cif, chain A (#17), sequence alignment score = 534
RMSD between 104 pruned atom pairs is 0.275 angstroms; (across all 104 pairs:
0.275)
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!15 models
> show #!14 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!14 models
> show #!15 models
> show #!14 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!15 models
> hide #!15 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!17 models
> select #17/A:75@NH2
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> select clear
> set bgColor white
> graphics silhouettes true
> lighting soft
> lighting soft depthCue true
> select #17/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #17/A:2
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #17/A:3
21 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel cartoons
> hide #!17 models
> show #!16 models
> select #16/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #16/A:2
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #16/A:3
21 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel cartoons
> hide #!16 models
> show #!15 models
> select clear
> select #15/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #15/A:2
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #15/A:3
21 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!14 models
> hide #!15 models
> select clear
> select #14/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #14/A:2
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #14/A:3
21 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel atoms
> hide sel cartoons
> show #!15 models
> hide #!14 models
> show #!14 models
> hide #!15 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> show #!17 models
> show #!15 models
> hide #!16 models
> hide #!17 models
> show #!14 models
> select #14/A:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select add #15/A:75
22 atoms, 20 bonds, 2 residues, 2 models selected
> show sel atoms
> show #!16 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> hide sel atoms
Drag select of 2 atoms, 2 bonds
> select up
4 atoms, 2 bonds, 2 residues, 2 models selected
> select up
16 atoms, 14 bonds, 2 residues, 2 models selected
> hide sel atoms
> hide #!14 models
> hide #!15 models
> show #!15 models
> hide #!15 models
> show #!14 models
> hide #!14 models
> show #!16 models
> show #!17 models
> hide #!16 models
> hide #!17 models
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sap_slam_fyn_wt/fold_sap_slam_fyn_model_0.cif
Chain information for fold_sap_slam_fyn_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> rename #17 AF3_sap_f77i_slam_2
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sapf77i_slam_fyn_wt/fold_sap_f77i_slam_fyn_model_0.cif
Chain information for fold_sap_f77i_slam_fyn_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> rename #16 AF3_sapwt_slam_2
> ui tool show Matchmaker
> undo
[Repeated 8 time(s)]
> hide #!15 models
> show #!16 models
> show #!17 models
> hide #!17 models
> hide #!16 models
> rename #2 id #18
> rename #6 id #19
> color bfactor #18 palette alphafold
1407 atoms, 176 residues, atom bfactor range 55.1 to 98.9
> color bfactor #19 palette alphafold
1404 atoms, 176 residues, atom bfactor range 55.2 to 98.9
> ui tool show Matchmaker
> matchmaker #18-19 to #14
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
fold_sap_slam_fyn_model_0.cif, chain A (#18), sequence alignment score = 535.4
RMSD between 104 pruned atom pairs is 0.000 angstroms; (across all 104 pairs:
0.000)
Matchmaker AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
fold_sap_f77i_slam_fyn_model_0.cif, chain A (#19), sequence alignment score =
531.2
RMSD between 104 pruned atom pairs is 0.257 angstroms; (across all 104 pairs:
0.257)
> select #18/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #19/A:77
19 atoms, 18 bonds, 2 residues, 2 models selected
> show sel atoms
> ui tool show Contacts
> select #18/A:77@CE2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 7 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
17 contacts
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!18 models
> select clear
> select up
4 atoms, 3 bonds, 1 residue, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
12 contacts
> select #19/C:16@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select down
8 atoms, 7 bonds, 1 residue, 1 model selected
> select down
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!18 models
> select #19/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #19/A:2
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #19/A:3
21 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show #!18 models
> hide #!19 models
> select #18/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #18/A:2
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #18/A:3
21 atoms, 18 bonds, 3 residues, 1 model selected
> hide sel cartoons
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> select #19/C:17
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> hide sel cartoons
> hide #!19 models
> show #!18 models
> select #18/C:48
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 5 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> hide sel cartoons
> save /home/rquiroga/colaboraciones/Eva/alphafold_preds.cxs
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!18 models
> show #!19 models
> select #19/A:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!18 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> show #!18 models
> hide #!18 models
> hide #!19 models
> show #!17 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!15 models
> hide #!15 models
> show #!14 models
> show #!15 models
> show #!18 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> hide #!15 models
> hide #!14 models
> show #!14 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!15 models
> show #!14 models
> ui tool show "Side View"
> rename #14 inter_AF3_sap_slam_fyn_model_0.cif
> rename #15 inter_AF3_sap_f77i_slam_fyn_model_0.cif
> rename #16 id #25
> rename #17 id #26
> rename #18 id #16
> rename #19 id #17
> rename #16 intra_AF3_sap_slam_fyn_model_0.cif
> rename #17 intra_AF3_sap_f77i_slam_fyn_model_0.cif
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sap_slam_fyn_wt/fold_sap_slam_fyn_model_0.cif
Chain information for fold_sap_slam_fyn_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sapf77i_slam_fyn_wt/fold_sap_f77i_slam_fyn_model_0.cif
Chain information for fold_sap_f77i_slam_fyn_model_0.cif #6
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> rename #2 id #18
> rename #6 id #19
> color bfactor #19 palette alphafold
1404 atoms, 176 residues, atom bfactor range 55.2 to 98.9
> color bfactor #18 palette alphafold
1407 atoms, 176 residues, atom bfactor range 55.1 to 98.9
> hide #!14 models
> hide #!15 models
> ui tool show Matchmaker
> matchmaker #18-19 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker intra_AF3_sap_slam_fyn_model_0.cif, chain A (#16) with
fold_sap_slam_fyn_model_0.cif, chain A (#18), sequence alignment score = 535.4
RMSD between 104 pruned atom pairs is 0.000 angstroms; (across all 104 pairs:
0.000)
Matchmaker intra_AF3_sap_slam_fyn_model_0.cif, chain A (#16) with
fold_sap_f77i_slam_fyn_model_0.cif, chain A (#19), sequence alignment score =
531.2
RMSD between 104 pruned atom pairs is 0.257 angstroms; (across all 104 pairs:
0.257)
> matchmaker #18-19 to #16
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker intra_AF3_sap_slam_fyn_model_0.cif, chain A (#16) with
fold_sap_slam_fyn_model_0.cif, chain A (#18), sequence alignment score = 535.4
RMSD between 104 pruned atom pairs is 0.000 angstroms; (across all 104 pairs:
0.000)
Matchmaker intra_AF3_sap_slam_fyn_model_0.cif, chain A (#16) with
fold_sap_f77i_slam_fyn_model_0.cif, chain A (#19), sequence alignment score =
531.2
RMSD between 104 pruned atom pairs is 0.257 angstroms; (across all 104 pairs:
0.257)
Drag select of 4 residues
> select up
315 atoms, 320 bonds, 38 residues, 2 models selected
> select up
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> select up
2811 atoms, 2876 bonds, 352 residues, 2 models selected
> select down
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> color #18 #813d9cff
> color #19 #813d9cff
> select clear
Drag select of 2 residues
> select up
308 atoms, 314 bonds, 36 residues, 2 models selected
> select up
984 atoms, 1010 bonds, 122 residues, 2 models selected
> ui tool show "Color Actions"
> color sel lime
> color sel lime green
Drag select of 2 residues
> show sel atoms
Drag select of 2 residues
> show sel atoms
Drag select of 8 residues
Drag select of 2 residues
> show sel atoms
> select #19/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #18/C:15
18 atoms, 16 bonds, 2 residues, 2 models selected
> show sel atoms
> select #18/C:17
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #19/C:17
16 atoms, 14 bonds, 2 residues, 2 models selected
> show sel atoms
Drag select of 2 residues
> show sel atoms
Drag select of 2 residues
> show sel atoms
> hide #19 models
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select up
1407 atoms, 1440 bonds, 176 residues, 1 model selected
> select down
492 atoms, 505 bonds, 61 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 interModel false distSlop 0.7 angleSlop 40.0 twoColors
> true intraMol false intraRes false select true reveal true retainCurrent
> true
13 hydrogen bonds found
6 strict hydrogen bonds found
> show #19 models
> hide #!18 models
> select clear
[Repeated 1 time(s)]
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> hbonds sel dashes 6 interModel false distSlop 0.7 angleSlop 40.0 twoColors
> true intraMol false intraRes false select true reveal true retainCurrent
> true
15 hydrogen bonds found
7 strict hydrogen bonds found
Drag select of 2 atoms, 2 bonds
> select add #19/A:81@NZ
3 atoms, 2 bonds, 2 residues, 1 model selected
> select add #19/A:82@OD1
4 atoms, 2 bonds, 3 residues, 1 model selected
> select add #19/A:82@ND2
5 atoms, 2 bonds, 3 residues, 1 model selected
> select up
18 atoms, 9 bonds, 8 residues, 1 model selected
> select up
74 atoms, 70 bonds, 8 residues, 1 model selected
> select down
18 atoms, 9 bonds, 8 residues, 1 model selected
> select up
74 atoms, 70 bonds, 8 residues, 1 model selected
> color sel byhetero
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!19 models
> show #!18 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
Drag select of 6 atoms, 6 bonds, 1 pseudobonds
> select add #18/C:17@OD1
7 atoms, 7 bonds, 1 pseudobond, 4 residues, 2 models selected
> select up
14 atoms, 8 bonds, 1 pseudobond, 6 residues, 2 models selected
> select up
54 atoms, 52 bonds, 1 pseudobond, 6 residues, 2 models selected
> select add #18/A:75@CZ
55 atoms, 52 bonds, 1 pseudobond, 7 residues, 2 models selected
> select add #18/A:78@CD
56 atoms, 52 bonds, 1 pseudobond, 8 residues, 2 models selected
> select up
76 atoms, 72 bonds, 1 pseudobond, 8 residues, 2 models selected
> color (#!18 & sel) byhetero
> ui tool show H-Bonds
> hbonds sel dashes 6 restrict both interModel false distSlop 0.7 angleSlop
> 40.0 twoColors true intraMol false intraRes false select true reveal true
> retainCurrent true
10 hydrogen bonds found
5 strict hydrogen bonds found
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!19 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> ui tool show "Build Structure"
> bond sel
Must specify two or more atoms
> torsion #18/A:82@CA@CB@CG@OD1 145.8
> torsion #18/A:82@CA@CB@CG@OD1 144.8
> torsion #18/A:82@CA@CB@CG@OD1 143.8
> torsion #18/A:82@CA@CB@CG@OD1 142.8
> torsion #18/A:82@CA@CB@CG@OD1 141.8
> torsion #18/A:82@CA@CB@CG@OD1 140.8
> torsion #18/A:82@CA@CB@CG@OD1 139.8
> torsion #18/A:82@CA@CB@CG@OD1 138.8
> torsion #18/A:82@CA@CB@CG@OD1 137.8
> torsion #18/A:82@CA@CB@CG@OD1 136.8
> torsion #18/A:82@CA@CB@CG@OD1 135.8
> torsion #18/A:82@CA@CB@CG@OD1 134.8
> torsion #18/A:82@CA@CB@CG@OD1 133.8
> torsion #18/A:82@CA@CB@CG@OD1 132.8
> torsion #18/A:82@CA@CB@CG@OD1 131.8
> torsion #18/A:82@CA@CB@CG@OD1 130.8
> torsion #18/A:82@CA@CB@CG@OD1 129.8
> torsion #18/A:82@CA@CB@CG@OD1 128.8
> torsion #18/A:82@CA@CB@CG@OD1 127.8
> torsion #18/A:82@CA@CB@CG@OD1 126.8
> torsion #18/A:82@CA@CB@CG@OD1 125.8
> torsion #18/A:82@CA@CB@CG@OD1 124.8
> torsion #18/A:82@CA@CB@CG@OD1 123.8
> torsion #18/A:82@CA@CB@CG@OD1 122.8
> torsion #18/A:82@CA@CB@CG@OD1 121.8
> torsion #18/A:82@CA@CB@CG@OD1 120.8
> torsion #18/A:82@CA@CB@CG@OD1 119.8
> torsion #18/A:82@CA@CB@CG@OD1 118.8
> torsion #18/A:82@CA@CB@CG@OD1 117.8
> torsion #18/A:82@CA@CB@CG@OD1 116.8
> torsion #18/A:82@CA@CB@CG@OD1 115.8
> torsion #18/A:82@CA@CB@CG@OD1 55.8
> torsion #18/A:82@CA@CB@CG@OD1 65.8
> show #!19 models
> torsion #18/A:82@CA@CB@CG@OD1 25.8
> torsion #18/A:82@CA@CB@CG@OD1 35.8
> torsion #18/A:82@CA@CB@CG@OD1 -5.8
> torsion #18/A:82@CA@CB@CG@OD1 -15.8
> torsion #18/A:82@CA@CB@CG@OD1 -17.8
> hide #!19 models
> select #18/C:49@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 5 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 restrict cross interModel false distSlop 0.7 angleSlop
> 40.0 twoColors true intraMol false intraRes false select true reveal true
> retainCurrent true
14 hydrogen bonds found
7 strict hydrogen bonds found
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> ui tool show "Build Structure"
> torsion #18/A:82@CA@CB@CG@OD1 -18.8
> torsion #18/A:82@CA@CB@CG@OD1 -19.8
> torsion #18/A:82@CA@CB@CG@OD1 -20.8
> torsion #18/A:82@CA@CB@CG@OD1 -21.8
> torsion #18/A:82@CA@CB@CG@OD1 -22.8
> torsion #18/A:82@CA@CB@CG@OD1 -23.8
> torsion #18/A:82@CA@CB@CG@OD1 -24.8
> torsion #18/A:82@CA@CB@CG@OD1 -25.8
> show #!19 models
> torsion #18/A:82@CA@CB@CG@OD1 -26.8
> select #19/C:49@OH
1 atom, 1 residue, 1 model selected
> hide #!19 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 5 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel dashes 6 restrict cross interModel false distSlop 0.7 angleSlop
> 40.0 twoColors true intraMol false intraRes false select true reveal true
> retainCurrent true
15 hydrogen bonds found
7 strict hydrogen bonds found
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> hide #!18 models
> hide #!19 models
> show #!18 models
> show #!19 models
> hide #!18 models
> hide #!19 models
> show #!16 models
> show #!17 models
> ui tool show Matchmaker
> matchmaker #!18 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sap_slam_fyn_model_0.cif, chain A
(#18), sequence alignment score = 524.6
RMSD between 102 pruned atom pairs is 0.384 angstroms; (across all 104 pairs:
0.746)
> matchmaker #!19 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sap_f77i_slam_fyn_model_0.cif, chain A
(#19), sequence alignment score = 520.4
RMSD between 101 pruned atom pairs is 0.465 angstroms; (across all 104 pairs:
0.869)
> matchmaker #!19 to #5
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 1m27, chain A (#5) with fold_sap_f77i_slam_fyn_model_0.cif, chain A
(#19), sequence alignment score = 520.4
RMSD between 101 pruned atom pairs is 0.465 angstroms; (across all 104 pairs:
0.869)
> show #!18 models
> show #!19 models
> hide #!16 models
> hide #!17 models
> select #19/A:87
11 atoms, 11 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #18/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #18/A:87
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> show #!16 models
> hide #!18 models
> hide #!19 models
> select #16/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #16/A:87
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> ui tool show Contacts
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
49 contacts
> hide #!16 models
> show #!17 models
> select #17/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #17/A:87
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> select up
21 atoms, 19 bonds, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true radius
> 0.025 reveal true
42 contacts
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
15 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #17/A:64
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #17/A:87@CD1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select down
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide #!17 models
> show #!18 models
> show #!19 models
> hide #!19 models
> select #18/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> select clear
> show #!19 models
> hide #!18 models
> show #!5 models
> hide #5.1 models
> hide #!5 models
> show #!18 models
> hide #!18 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel orange
> color sel byhetero
> select #19/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #19/A:87
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> color sel yellow
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!18 models
> hide #!19 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> select #18/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #18/A:87
19 atoms, 18 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> show #!19 models
> hide #!18 models
> select #19/A:64
14 atoms, 15 bonds, 1 residue, 1 model selected
> select clear
> select add #19/A:75@CZ
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
20 atoms, 18 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> show #!18 models
> hide #!19 models
> select #18/A:73
10 atoms, 10 bonds, 1 residue, 1 model selected
> show sel atoms
> hide sel atoms
> select #18/C:17@CB
1 atom, 1 residue, 1 model selected
> select add #18/A:78@CD
2 atoms, 2 residues, 1 model selected
> select up
19 atoms, 17 bonds, 2 residues, 1 model selected
> select up
266 atoms, 272 bonds, 31 residues, 1 model selected
> select down
19 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> hide #!18 models
> show #!19 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!19 models
> show #!19 models
> hide #!18 models
> select add #19/C:17@CG
1 atom, 1 bond, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 1 model selected
> select up
19 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> show #!18 models
> ui tool show "Side View"
> select #18/B:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 4 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> ui tool show "Color Actions"
> color sel gold
> color sel goldenrod
> hide #!19 models
> hide #!18 models
> show #!19 models
> select #19/B:6
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select down
90 atoms, 90 bonds, 11 residues, 1 model selected
> color sel goldenrod
> select clear
> select #19/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> hide #!19 models
> show #!18 models
> select #18/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> color sel byhetero
> select clear
> save /home/rquiroga/colaboraciones/Eva/paper1.cxs
> save /home/rquiroga/colaboraciones/Eva/wt_complex.jpg width 978 height 804
> supersample 3
> hide #!18 models
> show #!19 models
> save /home/rquiroga/colaboraciones/Eva/f77i_complex.jpg width 1216 height
> 1000 supersample 4
> hide #!19 models
> show #!18 models
> save /home/rquiroga/colaboraciones/Eva/wt_complex.jpg width 1216 height 1000
> supersample 3
> hide #!18 models
> show #!14 models
> hide #!14 models
> show #!15 models
> hide #!15 models
> show #!18 models
> hide #!18 models
> show #!16 models
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> color sel yellow
Drag select of 9 atoms, 8 bonds, 3 pseudobonds
> select up
30 atoms, 26 bonds, 3 pseudobonds, 5 residues, 3 models selected
> select up
43 atoms, 41 bonds, 3 pseudobonds, 5 residues, 3 models selected
> hide sel atoms
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
18 atoms, 17 bonds, 2 residues, 1 model selected
> hide sel atoms
> select #16/A:87
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #16/A:84
19 atoms, 18 bonds, 2 residues, 1 model selected
> show sel atoms
> select #16/A:64@CE2
1 atom, 1 residue, 1 model selected
> select up
14 atoms, 15 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!17 models
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 1 model selected
> color sel yellow
> select clear
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> show #!18 models
> hide #!18 models
> hide #!17 models
> hide #!16 models
> show #!17 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!17 models
> hide #!16 models
> show #!18 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!16 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!14 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!14 models
> show #!15 models
> select #15/C:16@CG
1 atom, 1 residue, 1 model selected
> select up
3 atoms, 1 bond, 2 residues, 2 models selected
> select up
17 atoms, 15 bonds, 2 residues, 2 models selected
> hide #!14 models
> hide #!15 models
> show #!18 models
> show #!19 models
> select #19/A:77@CG2
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> hide #!18 models
> hide #!19 models
> show #!17 models
> hide #!17 models
> show #!16 models
> hide #!16 models
> show #!18 models
> show #!19 models
> hide #!19 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel magenta
> select clear
> save /home/rquiroga/colaboraciones/Eva/paper2.cxs
> select #18/A:82@CG
1 atom, 1 residue, 1 model selected
> select add #18/C:16@OD1
2 atoms, 2 residues, 1 model selected
> select up
4 atoms, 1 bond, 3 residues, 1 model selected
> select up
28 atoms, 26 bonds, 3 residues, 1 model selected
> select add #18/A:78
39 atoms, 36 bonds, 4 residues, 1 model selected
> select add #18/A:79
48 atoms, 44 bonds, 5 residues, 1 model selected
> select up
351 atoms, 358 bonds, 42 residues, 1 model selected
> select down
48 atoms, 44 bonds, 5 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel radius 0.035 dashes 6 restrict cross interModel false distSlop
> 0.7 angleSlop 40.0 intraMol false intraRes false select true reveal true
> retainCurrent true
5 hydrogen bonds found
> select add #18/C:15
17 atoms, 8 bonds, 7 residues, 1 model selected
> select add #18/A:76
29 atoms, 20 bonds, 8 residues, 1 model selected
> select subtract #18/A:79
28 atoms, 20 bonds, 7 residues, 1 model selected
> select add #18/A:79
37 atoms, 28 bonds, 8 residues, 1 model selected
> select subtract #18/A:78
35 atoms, 28 bonds, 7 residues, 1 model selected
> select add #18/A:78
46 atoms, 38 bonds, 8 residues, 1 model selected
> select up
79 atoms, 74 bonds, 8 residues, 1 model selected
> hbonds sel radius 0.035 dashes 6 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false select true reveal true
> retainCurrent true
6 hydrogen bonds found
> select #18/C:49@CZ
1 atom, 1 residue, 1 model selected
> select clear
> select #18/C:49@CZ
1 atom, 1 residue, 1 model selected
Drag select of 3 atoms, 2 bonds
Drag select of 2 atoms, 2 bonds
> select add #18/A:79
14 atoms, 12 bonds, 3 residues, 1 model selected
> select add #18/A:76
26 atoms, 25 bonds, 4 residues, 1 model selected
> select add #18/C:15
35 atoms, 33 bonds, 5 residues, 1 model selected
> select up
40 atoms, 35 bonds, 6 residues, 1 model selected
> select up
61 atoms, 58 bonds, 6 residues, 1 model selected
> hbonds sel radius 0.035 dashes 6 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false select true reveal true
> retainCurrent true
4 hydrogen bonds found
Drag select of 2 atoms, 1 bonds, 1 pseudobonds
Drag select of 1 atoms, 2 bonds
Drag select of 1 atoms
Drag select of 6 atoms, 4 bonds, 2 pseudobonds
> select up
13 atoms, 7 bonds, 3 pseudobonds, 6 residues, 2 models selected
> select add #18/C:15
22 atoms, 15 bonds, 3 pseudobonds, 7 residues, 2 models selected
> select add #18/A:76
34 atoms, 27 bonds, 3 pseudobonds, 8 residues, 2 models selected
> select up
77 atoms, 74 bonds, 3 pseudobonds, 8 residues, 2 models selected
> select up
351 atoms, 358 bonds, 3 pseudobonds, 42 residues, 2 models selected
> select down
77 atoms, 74 bonds, 3 pseudobonds, 8 residues, 2 models selected
> hbonds sel radius 0.035 dashes 6 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
9 hydrogen bonds found
> select clear
[Repeated 1 time(s)]
> select #18/A:81@CE
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 1 model selected
> select down
9 atoms, 8 bonds, 1 residue, 1 model selected
> hide sel atoms
> hide #!18 models
> show #!19 models
Drag select of 1 atoms
[Repeated 1 time(s)]
> select add #19/A:77
10 atoms, 8 bonds, 3 residues, 1 model selected
> select add #19/A:79
19 atoms, 16 bonds, 4 residues, 1 model selected
> select add #19/A:78
30 atoms, 26 bonds, 5 residues, 1 model selected
> select add #19/A:76
42 atoms, 38 bonds, 6 residues, 1 model selected
> select add #19/C:15
51 atoms, 46 bonds, 7 residues, 1 model selected
> select up
53 atoms, 49 bonds, 8 residues, 1 model selected
> select up
77 atoms, 75 bonds, 8 residues, 1 model selected
> ui tool show H-Bonds
> hbonds sel radius 0.035 dashes 6 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
6 hydrogen bonds found
> hbonds sel radius 0.035 dashes 5 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
6 hydrogen bonds found
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
6 hydrogen bonds found
> hide #!19 models
> show #!18 models
> select #18/C:49@OH
1 atom, 1 residue, 1 model selected
> select add #18/C:16@CG
2 atoms, 1 bond, 2 residues, 1 model selected
> select add #18/A:79
11 atoms, 9 bonds, 3 residues, 1 model selected
> select add #18/A:78
22 atoms, 19 bonds, 4 residues, 1 model selected
> select add #18/C:17@CG
23 atoms, 19 bonds, 5 residues, 1 model selected
> select add #18/A:76
35 atoms, 31 bonds, 6 residues, 1 model selected
> select up
37 atoms, 32 bonds, 7 residues, 1 model selected
> select up
68 atoms, 65 bonds, 7 residues, 1 model selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
8 hydrogen bonds found
> show #!19 models
> hide #!19 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!18 models
> select clear
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!16 models
> show #!17 models
> hide #!17 models
> ui tool show Contacts
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select intersect C
24 atoms, 23 bonds, 3 residues, 1 model selected
> contacts sel restrict both interModel false ignoreHiddenModels true select
> true radius 0.025 reveal true
No contacts
> select clear
> select add #16/A:77@CZ
1 atom, 1 bond, 1 residue, 1 model selected
> select up
5 atoms, 2 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select intersect C
24 atoms, 23 bonds, 3 residues, 1 model selected
> contacts sel restrict both interModel false ignoreHiddenModels true select
> true radius 0.025 reveal true
No contacts
> select #16/A:13
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
6 atoms, 3 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select intersect C
24 atoms, 23 bonds, 3 residues, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
39 contacts
> select intersect C
39 atoms, 16 residues, 1 model selected
> contacts sel restrict both interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
35 contacts
> select #16/C:16@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select up
1407 atoms, 1440 bonds, 176 residues, 1 model selected
> select down
492 atoms, 505 bonds, 61 residues, 1 model selected
> hide sel atoms
> turn x 90
> turn x -90
> turn y 90
> turn y -90
[Repeated 1 time(s)]
> turn y 90
> turn z 90
> turn z -90
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> select clear
> select #16/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
> select #16/A:77@CE2
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 1 model selected
> select down
11 atoms, 11 bonds, 1 residue, 1 model selected
> color sel magenta
> hide #!16 models
> show #!17 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel yellow
> select clear
> select #17/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
109 atoms, 111 bonds, 13 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select up
22390 atoms, 21676 bonds, 3849 residues, 19 models selected
> select down
1404 atoms, 1436 bonds, 176 residues, 3 models selected
> select subtract #17/A:87
1393 atoms, 1423 bonds, 175 residues, 1 model selected
> select subtract #17/A:84
1385 atoms, 1414 bonds, 174 residues, 1 model selected
> select subtract #17/A:82
1377 atoms, 1405 bonds, 173 residues, 1 model selected
> select down
1377 atoms, 1404 bonds, 173 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select #17/A:87
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #17/A:84
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #17/A:82
27 atoms, 25 bonds, 3 residues, 1 model selected
> select up
29 atoms, 26 bonds, 4 residues, 1 model selected
> select up
35 atoms, 32 bonds, 4 residues, 1 model selected
> select ~sel & ##selected
1369 atoms, 1404 bonds, 40 pseudobonds, 172 residues, 2 models selected
> ui tool show "Color Actions"
> color sel medium purple
> color sel dark orchid
> color sel medium orchid
> color sel dark orchid
> show #!18 models
> hide #!18 models
> color #17 #813d9cff
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #17/A:84@CG2
9 atoms, 8 bonds, 2 residues, 1 model selected
> select up
11 atoms, 8 bonds, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> color sel yellow
> select clear
> show #!18 models
> hide #!18 models
> select #17/B:7
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> ui tool show "Color Actions"
> color sel goldenrod
> select clear
> show #!16 models
> hide #!17 models
> select #16/B:7
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> color sel goldenrod
> select add #16/A:87
101 atoms, 101 bonds, 12 residues, 1 model selected
> select add #16/A:84
109 atoms, 108 bonds, 13 residues, 1 model selected
> select add #16/A:82
117 atoms, 115 bonds, 14 residues, 1 model selected
> select up
119 atoms, 116 bonds, 15 residues, 1 model selected
> select up
128 atoms, 126 bonds, 15 residues, 1 model selected
> select ~sel & ##selected
1279 atoms, 1314 bonds, 35 pseudobonds, 161 residues, 2 models selected
> color (#!16 & sel) #813d9cff
> show #!17 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> select #17/A:77@CB
1 atom, 1 residue, 1 model selected
> select add #17/A:84@CD1
2 atoms, 1 bond, 2 residues, 1 model selected
> select up
4 atoms, 1 bond, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> select intersect C
21 atoms, 19 bonds, 3 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
33 contacts
> select intersect C
33 atoms, 15 residues, 1 model selected
> contacts sel restrict both interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
25 contacts
> select clear
> select up
4 atoms, 2 bonds, 2 residues, 1 model selected
> select up
15 atoms, 13 bonds, 2 residues, 1 model selected
> hide sel atoms
> select clear
> show #!16 models
> hide #!17 models
> select clear
> select #16/A:84@CD1
1 atom, 1 residue, 1 model selected
> select up
5 atoms, 2 bonds, 3 residues, 1 model selected
> select up
30 atoms, 29 bonds, 3 residues, 1 model selected
> select intersect C
24 atoms, 23 bonds, 3 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict cross interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
39 contacts
> select intersect C
39 atoms, 16 residues, 1 model selected
> contacts sel restrict both interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
35 contacts
> select clear
> select add #16/C:14@CB
1 atom, 1 residue, 1 model selected
> select #16/C:14@CG2
1 atom, 1 residue, 1 model selected
> select up
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select down
154 atoms, 157 bonds, 18 residues, 1 model selected
> hide sel atoms
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> select #17/A:82@CG
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide sel atoms
> show #!16 models
> hide #!17 models
> show #!17 models
> hide #!16 models
> show #!16 models
> hide #!17 models
> hide #!16 models
> show #!14 models
> show #!15 models
> hide #!14 models
> hide #!15 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!18 models
> hide #!18 models
> show #!19 models
> hide #!19 models
> show #!14 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!14 models
> show #!19 models
> hide #!19 models
> hide #!18 models
> show #!18 models
> show #!19 models
> show #!16 models
> hide #!16 models
> show #!17 models
> hide #!17 models
> show #!14 models
> show #!15 models
> hide #!18 models
> hide #!19 models
> show #!18 models
> hide #!18 models
Drag select of 8 residues
> select up
219 atoms, 218 bonds, 28 residues, 3 models selected
> select up
1806 atoms, 1851 bonds, 226 residues, 3 models selected
> select up
4215 atoms, 4312 bonds, 528 residues, 3 models selected
> select down
1806 atoms, 1851 bonds, 226 residues, 3 models selected
> color (#!14-15 & sel) lime
> show #!18 models
> hide #!18 models
> ui tool show "Color Actions"
> color sel lime green
> show #!17 models
> hide #!17 models
> color sel lime green
> color (#!14-15 & sel) byhetero
> select clear
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
Drag select of 28 residues
> select up
218 atoms, 107 bonds, 28 residues, 2 models selected
> select up
366 atoms, 366 bonds, 46 residues, 2 models selected
> select up
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> select down
366 atoms, 366 bonds, 46 residues, 2 models selected
> select up
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> ui tool show "Color Actions"
> select clear
Drag select of 4 residues
Drag select of 2 residues
> select up
436 atoms, 444 bonds, 56 residues, 2 models selected
> select up
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> color sel #9932ccff
> color sel #813d9cff
> select up
4 atoms, 2 bonds, 2 residues, 2 models selected
> select up
19 atoms, 18 bonds, 2 residues, 2 models selected
> color sel magenta
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #14/A:87
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #14/A:84
27 atoms, 25 bonds, 3 residues, 1 model selected
> color sel yellow
Drag select of 3 residues
> select up
136 atoms, 136 bonds, 17 residues, 2 models selected
> select clear
Drag select of 4 residues
> select up
64 atoms, 64 bonds, 8 residues, 2 models selected
> select up
180 atoms, 180 bonds, 22 residues, 2 models selected
> color sel goldenrod
> select clear
Drag select of 6 residues
> select up
94 atoms, 92 bonds, 12 residues, 2 models selected
> select up
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> select up
2811 atoms, 2876 bonds, 352 residues, 2 models selected
> select down
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> show sel surfaces
> hide #!15 models
> hide #14.2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> color (#!14 & sel) magenta
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #14/A:84
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #14/A:87
27 atoms, 25 bonds, 3 residues, 2 models selected
> color (#!14 & sel) yellow
> select clear
> show #14.2 models
> hide #!14 models
> show #!15 models
> hide #15.2 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> color (#!15 & sel) magenta
> select #15/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #15/A:84
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #15/A:87
27 atoms, 25 bonds, 3 residues, 2 models selected
> color (#!15 & sel) yellow
> show #15.2 models
> show #!14 models
> hide #!15 models
> turn z 90
> turn z -90
> turn y 90
> turn y -90
[Repeated 1 time(s)]
> turn y 90
> turn x 90
> turn x -90
> ui tool show "Side View"
> hide #!14.2 models
> select #14/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select up
1407 atoms, 1440 bonds, 176 residues, 2 models selected
> select down
825 atoms, 845 bonds, 104 residues, 2 models selected
> ui tool show Contacts
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035
141 contacts
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #14/A:54
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
62 atoms, 64 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> contacts sel restrict cross interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
141 contacts
> select clear
> select #14/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:48
829 atoms, 848 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
65 contacts
> select ~sel & ##selected
1347 atoms, 1402 bonds, 176 residues, 1 model selected
> hide sel atoms
> select #14/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:48
829 atoms, 848 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
65 contacts
> show sel atoms
> select up
153 atoms, 151 bonds, 16 residues, 2 models selected
> show sel atoms
> select clear
> show #14.2 models
> hide #14.2 models
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:48
829 atoms, 848 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
13 hydrogen bonds found
> select #14/A:31
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 47 bonds, 5 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:49
837 atoms, 857 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> select intersect C
314 atoms, 689 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #14/A:83
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:48
829 atoms, 848 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> select intersect C
314 atoms, 689 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
No contacts
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #14/C:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select add #14/A:82
500 atoms, 512 bonds, 62 residues, 1 model selected
> select up
539 atoms, 551 bonds, 67 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> select intersect C
314 atoms, 689 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #14/C:49@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 5 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select add #14/A:84
500 atoms, 512 bonds, 62 residues, 1 model selected
> select up
539 atoms, 551 bonds, 67 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> select up
1407 atoms, 1440 bonds, 176 residues, 2 models selected
> select down
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
13 hydrogen bonds found
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
13 hydrogen bonds found
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> color (#!14 & sel) byhetero
> show #!15 models
> hide #!14 models
> hide #15.2 models
> select #15/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> color (#!15 & sel) byhetero
> show #!14 models
> hide #!14 models
> show #!14 models
> select #15/A:80
8 atoms, 7 bonds, 1 residue, 1 model selected
> hide #!15 models
> show #!16 models
> hide #!14 models
> show #!14 models
> hide #!16 models
> show #!18 models
> hide #!18 models
> show #!18 models
> hide #!14 models
> ui tool show "Build Structure"
> hide #!18 models
> show #!14 models
> ui tool show "Build Structure"
> torsion #14/A:82@CA@CB@CG@OD1 -26.8
> ui tool show H-Bonds
> select #14/A:54
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
62 atoms, 64 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:49
837 atoms, 857 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
15 hydrogen bonds found
> select clear
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:50
833 atoms, 852 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> select intersect C
314 atoms, 689 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #14/A:69
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #14/C:49
837 atoms, 857 bonds, 105 residues, 2 models selected
> select up
863 atoms, 884 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> select clear
> select #14/A:69
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select #14/C:29
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
53 atoms, 53 bonds, 6 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select intersect C
314 atoms, 259 bonds, 61 residues, 1 model selected
> contacts sel interModel false intraMol false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
44 contacts
> select intersect C
21 atoms, 7 residues, 1 model selected
> select #14/A:57
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
22 atoms, 21 bonds, 3 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select intersect C
430 bonds, 1 model selected
> select #14/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select add #14/A:57
498 atoms, 510 bonds, 62 residues, 1 model selected
> select up
514 atoms, 526 bonds, 64 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> select intersect C
314 atoms, 689 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select up
827 atoms, 846 bonds, 105 residues, 2 models selected
> select up
837 atoms, 857 bonds, 105 residues, 2 models selected
> select intersect C
9 atoms, 439 bonds, 1 residue, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
No contacts
> select clear
> select #14/C:49@CE1
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 5 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select add #14/A:82
500 atoms, 512 bonds, 62 residues, 1 model selected
> select up
539 atoms, 551 bonds, 67 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
65 contacts
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
65 contacts
> select intersect C
21 atoms, 7 residues, 1 model selected
> save /home/rquiroga/colaboraciones/Eva/paper2.cxs
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select intersect C
430 bonds, 1 model selected
> select up
522 atoms, 430 bonds, 104 residues, 1 model selected
> select clear
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select up
1407 atoms, 1440 bonds, 176 residues, 2 models selected
> select down
825 atoms, 845 bonds, 104 residues, 2 models selected
> select intersect C
430 bonds, 1 model selected
> select clear
> select @C & #14
176 atoms, 176 residues, 1 model selected
> select clear
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select intersect C
430 bonds, 1 model selected
> select clear
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select @C
2659 atoms, 2659 residues, 19 models selected
> select clear
> select #14/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select clear
> select #14/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select down
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 10 bonds, 1 residue, 2 models selected
> select up
112 atoms, 115 bonds, 13 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select up
1407 atoms, 1440 bonds, 176 residues, 2 models selected
> select down
825 atoms, 845 bonds, 104 residues, 2 models selected
> hide #!14 models
> show #!16 models
> hide #!16 models
> show #!17 models
> show #!16 models
> hide #!16 models
> select #17/A:65
6 atoms, 5 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select down
822 atoms, 841 bonds, 104 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select down
822 atoms, 841 bonds, 104 residues, 1 model selected
> ui tool show "Color Actions"
> color sel #9932ccff
> color sel #813d9cff
> select #17/A:77@CG1
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> color sel magenta
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #17/A:84
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #17/A:87
27 atoms, 25 bonds, 3 residues, 1 model selected
> color sel yellow
> select clear
> show #!16 models
> select #17/B:10
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 4 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select down
90 atoms, 90 bonds, 11 residues, 1 model selected
> hide sel cartoons
> hide sel atoms
> select #16/B:9
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
35 atoms, 34 bonds, 4 residues, 1 model selected
> hide sel cartoons
> select #16/B:7
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
32 atoms, 32 bonds, 4 residues, 1 model selected
> select up
90 atoms, 90 bonds, 11 residues, 1 model selected
> select up
1407 atoms, 1440 bonds, 176 residues, 1 model selected
> select down
90 atoms, 90 bonds, 11 residues, 1 model selected
> hide sel cartoons
> hide #!16 models
> show #!16 models
> hide #!16 models
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select up
22390 atoms, 21676 bonds, 3849 residues, 19 models selected
> select up
22390 atoms, 21676 bonds, 3 pseudobonds, 3849 residues, 24 models selected
> select down
22390 atoms, 21676 bonds, 3849 residues, 23 models selected
> select down
1404 atoms, 1436 bonds, 176 residues, 5 models selected
> select down
822 atoms, 841 bonds, 104 residues, 1 model selected
> select down
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select up
1404 atoms, 1436 bonds, 176 residues, 1 model selected
> select down
822 atoms, 841 bonds, 104 residues, 1 model selected
> select intersect C
528 atoms, 426 bonds, 104 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select intersect C
528 atoms, 426 bonds, 104 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
No contacts
> select #17/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select intersect C
528 atoms, 426 bonds, 104 residues, 1 model selected
> contacts sel restrict both interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
199 contacts
> select up
721 atoms, 724 bonds, 89 residues, 1 model selected
> hide sel atoms
> select #17/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #17/A:82
16 atoms, 14 bonds, 2 residues, 1 model selected
> select add #17/A:84
24 atoms, 21 bonds, 3 residues, 1 model selected
> select add #17/A:87
35 atoms, 32 bonds, 4 residues, 1 model selected
> show sel atoms
> select #17/A:87
11 atoms, 11 bonds, 1 residue, 1 model selected
> select add #17/A:84
19 atoms, 18 bonds, 2 residues, 1 model selected
> select add #17/A:77@CB
20 atoms, 18 bonds, 3 residues, 1 model selected
> select up
27 atoms, 25 bonds, 3 residues, 1 model selected
> select intersect C
21 atoms, 19 bonds, 3 residues, 1 model selected
> contacts sel restrict cross interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
33 contacts
> select intersect C
33 atoms, 15 residues, 1 model selected
> contacts sel restrict both interModel false ignoreHiddenModels true select
> true dashes 7 radius 0.035 reveal true
25 contacts
> show #!16 models
> hide #!16 models
> hide #!17 models
> show #!14 models
> show #!15 models
> hide #!15 models
> save /home/rquiroga/colaboraciones/Eva/paper2.cxs
> select #14/A:86
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> hide #!14 models
> show #!15 models
> select #15/A:66
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 2 models selected
> select up
822 atoms, 841 bonds, 104 residues, 2 models selected
> hide #!15 models
> show #!16 models
> select #16/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> hide #!16 models
> show #!17 models
> select #17/A:67
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
109 atoms, 111 bonds, 13 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> hide #!17 models
> show #!18 models
> select #18/A:66
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> hide #!18 models
> show #!19 models
> select #19/A:66
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> hide #!19 models
> show #!14 models
> select #14/A:66
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select up
827 atoms, 846 bonds, 105 residues, 2 models selected
> select up
837 atoms, 857 bonds, 105 residues, 2 models selected
> select intersect C
9 atoms, 439 bonds, 1 residue, 1 model selected
> select clear
> select add #14
1407 atoms, 1440 bonds, 80 pseudobonds, 176 residues, 3 models selected
> select subtract #14
1 model selected
> select #14/A:86
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select intersect C
430 bonds, 1 model selected
> select clear
> close #25
> close #12-13
> close #7-8
> close #3,9-11
> save /home/rquiroga/colaboraciones/Eva/paper2.cxs
> select #14/A:68
7 atoms, 6 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> show #!15 models
> hide #!14 models
> select #15/A:66
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 2 models selected
> select up
822 atoms, 841 bonds, 104 residues, 2 models selected
> select intersect C
426 bonds, 1 model selected
> select clear
> rename #18 all_sap_slam_fyn_model_0.cif
> rename #19 all_AF3_sap_f77i_slam_fyn_model_0.cif
> rename #18 all_AF3_sap_slam_fyn_model_0.cif
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sap_slam_fyn_wt/fold_sap_slam_fyn_model_0.cif
Chain information for fold_sap_slam_fyn_model_0.cif #2
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> open
> /home/rquiroga/colaboraciones/Eva/alphafold3_sapf77i_slam_fyn_wt/fold_sap_f77i_slam_fyn_model_0.cif
Chain information for fold_sap_f77i_slam_fyn_model_0.cif #3
---
Chain | Description
A | .
B | .
C | .
Computing secondary structure
> rename #2 id #12
> rename #3 id #13
> ui tool show Matchmaker
> matchmaker #12-13#!15-17 to #14
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker inter_AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
fold_sap_slam_fyn_model_0.cif, chain A (#12), sequence alignment score = 535.4
RMSD between 104 pruned atom pairs is 0.000 angstroms; (across all 104 pairs:
0.000)
Matchmaker inter_AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
fold_sap_f77i_slam_fyn_model_0.cif, chain A (#13), sequence alignment score =
531.2
RMSD between 104 pruned atom pairs is 0.257 angstroms; (across all 104 pairs:
0.257)
Matchmaker inter_AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
inter_AF3_sap_f77i_slam_fyn_model_0.cif, chain A (#15), sequence alignment
score = 531.2
RMSD between 104 pruned atom pairs is 0.257 angstroms; (across all 104 pairs:
0.257)
Matchmaker inter_AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
intra_AF3_sap_slam_fyn_model_0.cif, chain A (#16), sequence alignment score =
535.4
RMSD between 104 pruned atom pairs is 0.000 angstroms; (across all 104 pairs:
0.000)
Matchmaker inter_AF3_sap_slam_fyn_model_0.cif, chain A (#14) with
intra_AF3_sap_f77i_slam_fyn_model_0.cif, chain A (#17), sequence alignment
score = 531.2
RMSD between 104 pruned atom pairs is 0.257 angstroms; (across all 104 pairs:
0.257)
> hide #!15 models
Drag select of 2 residues
> select up
221 atoms, 226 bonds, 26 residues, 2 models selected
> select up
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> select intersect C
1059 atoms, 856 bonds, 208 residues, 2 models selected
> select clear
Drag select of 4 residues
> select up
221 atoms, 226 bonds, 26 residues, 2 models selected
> select up
1647 atoms, 1686 bonds, 208 residues, 2 models selected
> ui tool show "Color Actions"
> color sel #9932ccff
> color sel #813d9cff
Drag select of 4 residues
> select up
308 atoms, 314 bonds, 36 residues, 2 models selected
> select up
984 atoms, 1010 bonds, 122 residues, 2 models selected
> color sel lime green
> select clear
Drag select of 4 residues
> select up
70 atoms, 68 bonds, 8 residues, 2 models selected
> select up
180 atoms, 180 bonds, 22 residues, 2 models selected
> color sel goldenrod
> select clear
Drag select of 2 residues
> color sel magenta
> select #12/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/A:82
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #12/A:84
24 atoms, 21 bonds, 3 residues, 2 models selected
> select add #13/A:83
32 atoms, 28 bonds, 4 residues, 2 models selected
> select subtract #13/A:83
24 atoms, 21 bonds, 3 residues, 2 models selected
> select add #13/A:84
32 atoms, 28 bonds, 4 residues, 2 models selected
> select add #12/A:87
43 atoms, 39 bonds, 5 residues, 2 models selected
> select add #13/A:87
54 atoms, 50 bonds, 6 residues, 2 models selected
> color sel yellow
> select clear
> show #!14 models
> hide #!14 models
> hide #13 models
> select #12/A:75
11 atoms, 10 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> select add #12/C:48
829 atoms, 848 bonds, 105 residues, 1 model selected
> select up
863 atoms, 884 bonds, 109 residues, 1 model selected
> select up
1317 atoms, 1350 bonds, 165 residues, 1 model selected
> select intersect C
845 atoms, 689 bonds, 165 residues, 1 model selected
> ui tool show Contacts
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
23 contacts
> hide #!12 models
> show #13 models
> select #13/A:84
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select add #13/C:48
826 atoms, 844 bonds, 105 residues, 1 model selected
> select up
860 atoms, 880 bonds, 109 residues, 1 model selected
> select up
1314 atoms, 1346 bonds, 165 residues, 1 model selected
> select intersect C
842 atoms, 685 bonds, 165 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
15 contacts
> select clear
> select #13/A:66
5 atoms, 4 bonds, 1 residue, 1 model selected
> select up
25 atoms, 26 bonds, 3 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select add #13/C:39
827 atoms, 845 bonds, 105 residues, 1 model selected
> select up
881 atoms, 903 bonds, 110 residues, 1 model selected
> select up
1314 atoms, 1346 bonds, 165 residues, 1 model selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true retainCurrent true
15 hydrogen bonds found
> select clear
> select add #13/A:1
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/C:33
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
122 atoms, 122 bonds, 17 residues, 1 model selected
> select up
1314 atoms, 1346 bonds, 165 residues, 1 model selected
> color sel byhetero
> select clear
> hide #!13 models
> show #!12 models
> select #12/C:38
9 atoms, 8 bonds, 1 residue, 1 model selected
> select add #12/A:82
17 atoms, 15 bonds, 2 residues, 1 model selected
> select up
106 atoms, 108 bonds, 12 residues, 1 model selected
> select up
1317 atoms, 1350 bonds, 165 residues, 1 model selected
> select up
1407 atoms, 1440 bonds, 176 residues, 1 model selected
> select down
1317 atoms, 1350 bonds, 165 residues, 1 model selected
> select down
106 atoms, 108 bonds, 12 residues, 1 model selected
> select up
1317 atoms, 1350 bonds, 165 residues, 1 model selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false select true reveal true
> retainCurrent true
13 hydrogen bonds found
> color sel byhetero
> select clear
> save /home/rquiroga/colaboraciones/Eva/paper2.cxs
——— End of log from Thu Jun 25 10:29:56 2026 ———
> view name session-start
opened ChimeraX session
> select #12/A:87
11 atoms, 11 bonds, 1 residue, 1 model selected
> select up
25 atoms, 25 bonds, 3 residues, 1 model selected
> select up
825 atoms, 845 bonds, 104 residues, 1 model selected
> surface sel
> hide #12.3 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> color (#!12 & sel) magenta
> color (#!12 & sel) byhetero
> select #12/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #12/A:84
16 atoms, 14 bonds, 2 residues, 2 models selected
> select add #12/A:87
27 atoms, 25 bonds, 3 residues, 2 models selected
> color (#!12 & sel) yellow
> color (#!12 & sel) byhetero
> show #12.3 models
> hide #12.3 models
> ui tool show "Build Structure"
> torsion #12/A:82@CA@CB@CG@OD1 -26.8
> ui tool show H-Bonds
> select #12/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
47 atoms, 46 bonds, 6 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> select add #12/C:46
834 atoms, 853 bonds, 105 residues, 2 models selected
> select up
860 atoms, 879 bonds, 109 residues, 2 models selected
> select up
1317 atoms, 1350 bonds, 165 residues, 2 models selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false select true reveal true
> retainCurrent true
15 hydrogen bonds found
> select clear
> show #12.3 models
> hide #12.3 models
> hide #!12 models
> show #!13 models
> select clear
> select #13/C:49@CD2
1 atom, 1 residue, 1 model selected
> select add #13/A:79
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
21 atoms, 20 bonds, 2 residues, 1 model selected
> select up
147 atoms, 150 bonds, 18 residues, 1 model selected
> select up
1314 atoms, 1346 bonds, 165 residues, 1 model selected
> select down
147 atoms, 150 bonds, 18 residues, 1 model selected
> select up
1314 atoms, 1346 bonds, 165 residues, 1 model selected
> hide sel atoms
> select #13/A:77
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select #13/A:77@CB
1 atom, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select add #13/C:16
16 atoms, 14 bonds, 2 residues, 1 model selected
> select up
263 atoms, 268 bonds, 31 residues, 1 model selected
> select up
1314 atoms, 1346 bonds, 165 residues, 1 model selected
> select down
263 atoms, 268 bonds, 31 residues, 1 model selected
> select down
16 atoms, 14 bonds, 2 residues, 1 model selected
> select clear
> select #13/C:48
4 atoms, 3 bonds, 1 residue, 1 model selected
> select up
38 atoms, 39 bonds, 5 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select up
494 atoms, 506 bonds, 62 residues, 1 model selected
> select up
500 atoms, 512 bonds, 62 residues, 1 model selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false select true reveal true
> retainCurrent true
0 hydrogen bonds found
> select #13/C:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select up
494 atoms, 506 bonds, 62 residues, 1 model selected
> select up
500 atoms, 512 bonds, 62 residues, 1 model selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true
0 hydrogen bonds found
> ui tool show Contacts
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
5 contacts
> ui tool show Contacts
> hide #!13 models
> show #!12 models
> select #12/C:37
14 atoms, 15 bonds, 1 residue, 1 model selected
> select up
59 atoms, 62 bonds, 6 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> hide sel atoms
> select #12/A:79
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
112 atoms, 115 bonds, 13 residues, 2 models selected
> select up
825 atoms, 845 bonds, 104 residues, 2 models selected
> hide sel atoms
> select #12/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select add #12/A:77
503 atoms, 516 bonds, 62 residues, 1 model selected
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true
0 hydrogen bonds found
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true select true dashes 7 radius 0.035 reveal true
6 contacts
> select add #12/C:15@CD
1 atom, 1 bond, 1 residue, 1 model selected
> select up
5 atoms, 2 bonds, 3 residues, 1 model selected
> select up
24 atoms, 23 bonds, 3 residues, 1 model selected
> color sel byhetero
> select clear
> hide #!12 models
> show #!13 models
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
109 atoms, 111 bonds, 13 residues, 1 model selected
> select up
822 atoms, 841 bonds, 104 residues, 1 model selected
> select add #13/C:16
830 atoms, 848 bonds, 105 residues, 1 model selected
> select up
976 atoms, 998 bonds, 122 residues, 1 model selected
> select up
1314 atoms, 1346 bonds, 165 residues, 1 model selected
> select clear
> select #13/C:16
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select subtract C
178 atoms, 61 residues, 1 model selected
> select up
180 atoms, 1 bond, 62 residues, 1 model selected
> select up
500 atoms, 512 bonds, 62 residues, 1 model selected
> select down
180 atoms, 1 bond, 62 residues, 1 model selected
> select add #13/A:77@CG2
181 atoms, 1 bond, 62 residues, 1 model selected
> select add #13/A:77@CB
182 atoms, 1 bond, 62 residues, 1 model selected
> select subtract #13/A:77
178 atoms, 61 residues, 1 model selected
> select add #13/A:77
186 atoms, 7 bonds, 62 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true color #e01b24 dashes 7 radius 0.035 reveal true
3 contacts
> contacts sel setAttrs true attrName "bad contacts" restrict both interModel
> false intraMol false ignoreHiddenModels true color #e01b24 dashes 7 radius
> 0.035 name "bad contacts" reveal true
Invalid "attrName" argument: Attribute names can consist only of alphanumeric
characters and underscores
> contacts sel setAttrs true attrName "bad contacts" restrict both interModel
> false intraMol false ignoreHiddenModels true color #e01b24 dashes 7 radius
> 0.035 name bad_contacts reveal true
Invalid "attrName" argument: Attribute names can consist only of alphanumeric
characters and underscores
> contacts sel setAttrs true attrName "bad contacts" restrict both interModel
> false intraMol false ignoreHiddenModels true color #e01b24 dashes 7 radius
> 0.035 name badcontacts reveal true
Invalid "attrName" argument: Attribute names can consist only of alphanumeric
characters and underscores
> contacts sel setAttrs true attrName badcontacts restrict both interModel
> false intraMol false ignoreHiddenModels true color #e01b24 dashes 7 radius
> 0.035 name badcontacts reveal true
3 contacts
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select up
494 atoms, 506 bonds, 62 residues, 1 model selected
> select up
500 atoms, 512 bonds, 62 residues, 1 model selected
> select intersect C
320 atoms, 264 bonds, 62 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
2 contacts
> hide #!13 models
> show #!12 models
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select up
494 atoms, 506 bonds, 62 residues, 1 model selected
> select up
503 atoms, 516 bonds, 62 residues, 2 models selected
> select intersect C
314 atoms, 268 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
No contacts
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
10 atoms, 8 bonds, 2 residues, 1 model selected
> select up
19 atoms, 18 bonds, 2 residues, 2 models selected
> select clear
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select up
494 atoms, 506 bonds, 62 residues, 1 model selected
> select up
503 atoms, 516 bonds, 62 residues, 2 models selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
6 contacts
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select subtract C
58 atoms, 18 residues, 1 model selected
> name frozen no_C_Fyn sel
> select #12/A:77@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select intersect C
9 bonds, 1 model selected
> select add no_C_Fyn
58 atoms, 9 bonds, 18 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true color #e01b24 dashes 7 radius 0.035 name badcontacts
> reveal true
No contacts
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true color #e01b24 dashes 7 radius 0.035 name badcontacts
> reveal true
No contacts
> select clear
> select #12/A:77@CE1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select add #12/C:15
20 atoms, 19 bonds, 2 residues, 2 models selected
> select clear
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select ~sel
16080 atoms, 16182 bonds, 203 pseudobonds, 2239 residues, 24 models selected
> select clear
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select add #12/A:77
503 atoms, 516 bonds, 62 residues, 1 model selected
> select intersect C
314 atoms, 268 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
No contacts
> select clear
> select #12/A:77@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select up
13 atoms, 12 bonds, 2 residues, 2 models selected
> select up
20 atoms, 19 bonds, 2 residues, 2 models selected
> select up
266 atoms, 272 bonds, 31 residues, 2 models selected
> select clear
> select #12/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select add #12/A:77
503 atoms, 516 bonds, 62 residues, 1 model selected
> select intersect C
314 atoms, 268 bonds, 61 residues, 1 model selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
No contacts
> select clear
> select #12/C:15@CB
1 atom, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
492 atoms, 505 bonds, 61 residues, 1 model selected
> select intersect C
314 atoms, 259 bonds, 61 residues, 1 model selected
> name frozen C_Fyn sel
> select #12/A:77@CZ
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select intersect C
9 bonds, 1 model selected
> select clear
> select #12/A:77
11 atoms, 11 bonds, 1 residue, 1 model selected
> hide sel cartoons
> select subtract #12/A:77@N
10 atoms, 10 bonds, 1 residue, 2 models selected
> select subtract #12/A:77@O
9 atoms, 9 bonds, 1 residue, 2 models selected
> select add C_Fyn
323 atoms, 268 bonds, 62 residues, 2 models selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true dashes 7 radius 0.035 reveal true
5 contacts
> select clear
> select #12/A:77@CE1
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> select subtract #12/A:77@O
10 atoms, 10 bonds, 1 residue, 2 models selected
> select subtract #12/A:77@N
9 atoms, 9 bonds, 1 residue, 2 models selected
> select add no_C_Fyn
67 atoms, 9 bonds, 19 residues, 2 models selected
> contacts sel restrict both interModel false intraMol false
> ignoreHiddenModels true color #e01b24 dashes 7 radius 0.035 name badcontacts
> reveal true
1 contacts
> hide #!12 models
> show #!12 models
> show #!13 models
> hide #!12 models
> close #14-15
> save /home/rquiroga/colaboraciones/Eva/paper2.cxs
> hide #!13 models
> show #!18 models
> show #!19 models
> hide #!19 models
> save /home/rquiroga/colaboraciones/Eva/paper3.cxs
[Repeated 1 time(s)]
> ui tool show Scenes
> scenes save zoom_out
> scenes restore zoom_out
> hide #!18 models
> show #!16 models
> ui tool show "Side View"
> scenes save intra
> scenes restore intra
> scenes restore zoom_out
> scenes restore intra
> scenes restore zoom_out
> ui tool show "Model Panel"
> hide #!18 models
> show #!12 models
> show #!13 models
> hide #!13 models
> select clear
> select #12/A:77@CA
1 atom, 1 residue, 1 model selected
> select up
11 atoms, 11 bonds, 1 residue, 2 models selected
> show sel cartoons
> select clear
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!12 models
> hide #!12 models
> show #!13 models
> hide #!13 models
> show #!13 models
> show #!12 models
> hide #!12 models
> select #13/C:15
9 atoms, 8 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> hide #!13 models
> show #!12 models
> scenes save inter
> select #12/A:82
8 atoms, 7 bonds, 1 residue, 1 model selected
> show sel atoms
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
8 atoms, 7 bonds, 1 residue, 2 models selected
> select add #12/C:16@CG
9 atoms, 7 bonds, 2 residues, 2 models selected
> select up
16 atoms, 14 bonds, 2 residues, 2 models selected
> select up
201 atoms, 203 bonds, 24 residues, 2 models selected
> select clear
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
9 atoms, 8 bonds, 1 residue, 1 model selected
> select up
154 atoms, 157 bonds, 18 residues, 1 model selected
> select up
156 atoms, 158 bonds, 19 residues, 1 model selected
> select up
162 atoms, 164 bonds, 19 residues, 2 models selected
> ui tool show H-Bonds
> hbonds sel radius 0.035 dashes 7 restrict both interModel false distSlop 0.7
> angleSlop 40.0 intraMol false intraRes false reveal true
1 hydrogen bonds found
> select clear
> scenes restore inter
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/tool.py", line 161, in scene_selected_cb
run(self.session, f"scene restore {StringArg.unparse(scene_name)}")
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/cmd.py", line 61, in restore_scene
session.scenes.restore_scene(scene_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/manager.py", line 102, in restore_scene
self.get_scene(scene_name).restore_scene()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/scene.py", line 198, in restore_scene
model.restore_scene(scene_data)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 370, in restore_scene
pseudobonds.colors = pb_state['colors']
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 0 does not match objects array length 1
Error processing trigger "scene selected":
ValueError: Values array length 0 does not match objects array length 1
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
> scenes save inter
> scenes restore intra
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/tool.py", line 161, in scene_selected_cb
run(self.session, f"scene restore {StringArg.unparse(scene_name)}")
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/cmd.py", line 61, in restore_scene
session.scenes.restore_scene(scene_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/manager.py", line 102, in restore_scene
self.get_scene(scene_name).restore_scene()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/scene.py", line 198, in restore_scene
model.restore_scene(scene_data)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 370, in restore_scene
pseudobonds.colors = pb_state['colors']
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 0 does not match objects array length 1
Error processing trigger "scene selected":
ValueError: Values array length 0 does not match objects array length 1
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
> scenes restore zoom_out
Traceback (most recent call last):
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/triggerset.py", line 149, in invoke
return self._func(self._name, data)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/tool.py", line 161, in scene_selected_cb
run(self.session, f"scene restore {StringArg.unparse(scene_name)}")
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3245, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/cmd.py", line 61, in restore_scene
session.scenes.restore_scene(scene_name)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/manager.py", line 102, in restore_scene
self.get_scene(scene_name).restore_scene()
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/scenes/scene.py", line 198, in restore_scene
model.restore_scene(scene_data)
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/pbgroup.py", line 370, in restore_scene
pseudobonds.colors = pb_state['colors']
^^^^^^^^^^^^^^^^^^
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
ValueError: Values array length 0 does not match objects array length 1
Error processing trigger "scene selected":
ValueError: Values array length 0 does not match objects array length 1
File "/usr/lib/ucsf-chimerax/lib/python3.11/site-
packages/chimerax/atomic/molc.py", line 226, in set_prop
raise ValueError('Values array length %d does not match objects array length
%d'
See log for complete Python traceback.
OpenGL version: 3.3.0 NVIDIA 550.144.03
OpenGL renderer: NVIDIA GeForce GTX 1080/PCIe/SSE2
OpenGL vendor: NVIDIA Corporation
Python: 3.11.13
Locale: en_US.UTF-8
Qt version: PyQt6 6.10.2, Qt 6.10.0
Qt runtime version: 6.10.2
Qt platform: xcb
XDG_SESSION_TYPE=x11
DESKTOP_SESSION=ubuntu
XDG_SESSION_DESKTOP=ubuntu
XDG_CURRENT_DESKTOP=ubuntu:GNOME
DISPLAY=:1
Manufacturer: Gigabyte Technology Co., Ltd.
Model: B550M AORUS ELITE
OS: Ubuntu 22.04
Architecture: 64bit ELF
Virtual Machine: none
CPU: 24 AMD Ryzen 9 5900X 12-Core Processor
Cache Size: 512 KB
Memory:
total used free shared buff/cache available
Mem: 62Gi 16Gi 29Gi 363Mi 17Gi 47Gi
Swap: 2.0Gi 0B 2.0Gi
Graphics:
07:00.0 VGA compatible controller [0300]: NVIDIA Corporation GP104 [GeForce GTX 1080] [10de:1b80] (rev a1)
Subsystem: Micro-Star International Co., Ltd. [MSI] GP104 [GeForce GTX 1080] [1462:3367]
Kernel driver in use: nvidia
Installed Packages:
accessible-pygments: 0.0.5
aiohappyeyeballs: 2.6.2
aiohttp: 3.13.4
aiosignal: 1.4.0
alabaster: 1.0.0
annotated-types: 0.7.0
anyio: 4.13.0
appdirs: 1.4.4
asttokens: 3.0.1
attrs: 26.1.0
babel: 2.18.0
beautifulsoup4: 4.13.5
blockdiag: 3.0.0
blosc2: 4.4.3
bs4: 0.0.2
build: 1.3.0
certifi: 2026.5.20
cftime: 1.6.5
charset-normalizer: 3.4.7
ChimeraX-AddCharge: 1.5.20
ChimeraX-AddH: 2.2.8
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.6.2
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 3.2
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Animations: 1.0
ChimeraX-Aniso: 1.3.2
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.67.1
ChimeraX-AtomicLibrary: 14.4
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.3
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-Boltz: 1.1
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.2
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.6.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4.1
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.5
ChimeraX-ChemGroup: 2.0.2
ChimeraX-Clashes: 2.4
ChimeraX-Cluster: 1.0
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.8
ChimeraX-CommandLine: 1.3.1
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.12
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.5
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.4
ChimeraX-Dicom: 1.2.7
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.2.2
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5.3
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.4
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.8.2
ChimeraX-Label: 1.5
ChimeraX-LightingGUI: 1.0
ChimeraX-LinuxSupport: 1.0.1
ChimeraX-ListInfo: 1.3.1
ChimeraX-Log: 1.2.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.3
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchAlign: 1.2
ChimeraX-MatchMaker: 2.4.1
ChimeraX-MCopy: 1.0
ChimeraX-MCPServer: 0.2.0
ChimeraX-MDcrds: 2.19
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-Minimize: 1.3.9
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.16
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.23
ChimeraX-ModelPanel: 1.6.1
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0.1
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.15.4
ChimeraX-OpenFold: 1.0
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.13
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.5
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.4
ChimeraX-ProfileGrids: 1.6
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.8.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.3
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.2
ChimeraX-Scenes: 0.3.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.3
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.12
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.18
ChimeraX-Shape: 1.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.1
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SNFG: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.19.3
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5.3
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.4
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.50.8
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.2
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDock: 1.6.2
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.5
ChimeraX-Zone: 1.0.1
click: 8.4.1
colorama: 0.4.6
comm: 0.2.3
contourpy: 1.3.3
coverage: 7.14.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.2.4
debugpy: 1.8.21
decorator: 5.3.1
distro: 1.9.0
docutils: 0.21.2
executing: 2.2.1
filelock: 3.19.1
fonttools: 4.63.0
frozenlist: 1.8.0
funcparserlib: 2.0.0a0
glfw: 2.10.0
grako: 3.16.5
h11: 0.16.0
h5py: 3.16.0
html2text: 2025.4.15
httpcore: 1.0.9
httpx: 0.28.1
httpx-sse: 0.4.3
idna: 3.18
ihm: 2.2
imagecodecs: 2024.6.1
imagesize: 2.0.0
iniconfig: 2.3.0
ipykernel: 7.1.0
ipython: 9.9.0
ipython_pygments_lexers: 1.1.1
jedi: 0.19.2
Jinja2: 3.1.6
jsonschema: 4.26.0
jsonschema-specifications: 2025.9.1
jupyter_client: 8.8.0
jupyter_core: 5.9.1
kiwisolver: 1.5.0
line_profiler: 5.0.0
lxml: 6.0.2
lz4: 4.3.2
Markdown: 3.8.2
MarkupSafe: 3.0.3
matplotlib: 3.10.7
matplotlib-inline: 0.2.2
mcp: 1.18.0
msgpack: 1.1.1
multidict: 6.7.1
narwhals: 2.22.1
ndindex: 1.10.1
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.14.1
numpy: 1.26.4
nvidia-nvjitlink-cu12: 12.9.86
OpenMM: 8.4.0
OpenMM-CUDA-12: 8.4.0
openvr: 1.26.701
packaging: 25.0
ParmEd: 4.2.2
parso: 0.8.7
pep517: 0.13.1
pexpect: 4.9.0
pickleshare: 0.7.5
pillow: 11.3.0
pip: 25.2
pkginfo: 1.12.1.2
platformdirs: 4.10.0
plotly: 6.8.0
pluggy: 1.6.0
prompt_toolkit: 3.0.52
propcache: 0.5.2
psutil: 7.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pybind11: 3.0.1
pycollada: 0.8
pydantic: 2.13.4
pydantic-settings: 2.14.1
pydantic_core: 2.46.4
pydata-sphinx-theme: 0.18.0
pydicom: 2.4.4
Pygments: 2.18.0
pynmrstar: 3.5.1
pynrrd: 1.0.0
PyOpenGL: 3.1.10
PyOpenGL-accelerate: 3.1.10
pyopenxr: 1.1.4501
pyparsing: 3.3.2
pyproject_hooks: 1.2.0
PyQt6: 6.10.2
PyQt6-Qt6: 6.10.2
PyQt6-WebEngine: 6.10.0
PyQt6-WebEngine-Qt6: 6.10.2
PyQt6_sip: 13.10.3
pytest: 9.0.3
pytest-cov: 7.1.0
python-dateutil: 2.9.0.post0
python-dotenv: 1.2.2
python-multipart: 0.0.32
pyzmq: 27.1.0
qtconsole: 5.7.0
QtPy: 2.4.3
qtshim: 1.2.2
RandomWords: 0.4.0
referencing: 0.37.0
requests: 2.32.5
roman-numerals: 4.1.0
rpds-py: 2026.5.1
scipy: 1.14.0
setuptools: 80.9.0
sfftk-rw: 0.8.1
six: 1.17.0
snowballstemmer: 3.1.1
sortedcontainers: 2.4.0
soupsieve: 2.8.4
Sphinx: 9.0.4
sphinx-autodoc-typehints: 3.6.1
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
sse-starlette: 3.4.4
stack-data: 0.6.3
starlette: 1.3.0
superqt: 0.7.6
tables: 3.10.2
tcia_utils: 3.2.1
threadpoolctl: 3.6.0
tifffile: 2025.3.13
tinyarray: 1.2.5
tornado: 6.5.7
tqdm: 4.68.2
traitlets: 5.14.3
typing-inspection: 0.4.2
typing_extensions: 4.15.0
Unidecode: 1.4.0
urllib3: 2.7.0
uvicorn: 0.49.0
wcwidth: 0.8.1
webcolors: 24.11.1
wheel: 0.45.1
wheel-filename: 1.4.2
yarl: 1.24.2
Change History (1)
comment:1 by , 43 hours ago
| Cc: | added |
|---|---|
| Component: | Unassigned → Scenes/Animation |
| Description: | modified (diff) |
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → accepted |
| Summary: | ChimeraX bug report submission → Problem restoring pseudo bonds in scenes |
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